Package 'ribd'

Basic relationships

Description

A data frame containing kinship and kappa coefficients for some commonly used relationships.

Usage

basicRelationships

Format

A data frame with 12 rows and 7 columns. The last column (pos) is used internally for placing labels on triangle plots.

Details

label	relationship	phi	kappa0	kappa1	kappa2	pos
UN	unrelated	0.000000	1.00000	0.0000	0.00000	1
PO	parent-offspring	0.250000	0.00000	1.0000	0.00000	1
MZ	monozygotic twins	0.500000	0.00000	0.0000	1.00000	4
S	full siblings	0.250000	0.25000	0.5000	0.25000	4
H	half siblings	0.125000	0.50000	0.5000	0.00000	1
A	avuncular	0.125000	0.50000	0.5000	0.00000	1
G	grandparent-grandchild	0.125000	0.50000	0.5000	0.00000	1
H,U,G	halfsib/uncle/grandp	0.125000	0.50000	0.5000	0.00000	1
FC	first cousins	0.062500	0.75000	0.2500	0.00000	1
SC	second cousins	0.015625	0.93750	0.0625	0.00000	1
DFC	double first cousins	0.125000	0.56250	0.3750	0.06250	3
Q	quad half first cousins	0.125000	0.53125	0.4375	0.03125	4

---

Table of pairwise relatedness coefficients

Description

Creates a data frame containing various relatedness coefficients between all pairs of individuals in a given pedigree.

Usage

coeffTable(
  x,
  ids = labels(x),
  coeff = c("f", "phi", "deg", "kappa", "identity", "detailed"),
  self = FALSE,
  Xchrom = FALSE
)

Arguments

x	A pedigree in the form of a pedtools::ped object.
ids	A character (or coercible to character) containing ID labels of two or more pedigree members.
coeff	A character vector containing one or more of the keywords "f", "phi", "deg", "kappa", "identity", "detailed".
self	A logical indicating if self-relationships should be included. Default: FALSE.
Xchrom	A logical indicating if the coefficients should be autosomal (default) or X-chromosomal. If Xchrom = NA, both sets are included.

Details

Available coefficients (indicated in coeff) include:

• f: The inbreeding coefficient of each pair member. Columns: f1 and f2.

• phi: The kinship coefficient. Column: phi.

• deg: The degree of relationship, as computed by kin2deg. Column: deg

• kappa: The IBD coefficients computed by kappaIBD. (These are NA for pairs involving inbred individuals.) Columns: k0, k1, k2.

• identity: The 9 condensed identity coefficients of Jacquard, computed by identityCoefs(). Columns: D1, ..., D9.

• detailed: The detailed identity coefficients of Jacquard, computed by identityCoefs(..., detailed = TRUE). Columns: d1, ..., d15.

Value

A data frame with one row for each pair of individuals. The first two columns are characters named id1 and id2, while remaining columns are numeric. Columns containing X-chromosomal coefficients are suffixed with ".X".

If "f" (inbreeding) is the only coefficient, the data frame has one row per individual, and the first column is named id.

Note: If x has members with unknown sex, all X-chromosomal coefficients are NA.

Examples

# Uncle-nephew pedigree
x = avuncularPed()

# Complete table
coeffTable(x)

# Only selected coefficients
coeffTable(x, coeff = c("phi", "deg", "kappa"))

# Only the uncle-nephew pair
coeffTable(x, ids = c(3, 6), coeff = c("phi", "deg", "kappa"))

# X-chromosomal coefficients
coeffTable(x, Xchrom = TRUE, coeff = "kappa")

# Both autosomal and X
coeffTable(x, Xchrom = NA, coeff = "phi")

---

Condensed identity coefficients

Description

Computes the 9 condensed identity coefficients of pairwise relationships in a pedigree. Founders of the pedigree may be inbred; use pedtools::founderInbreeding() to set this up.

Usage

condensedIdentity(
  x,
  ids,
  sparse = NA,
  simplify = TRUE,
  self = FALSE,
  verbose = FALSE
)

Arguments

x	A pedigree in the form of a pedtools::ped object
ids	A character (or coercible to character) containing ID labels of two or more pedigree members.
sparse	A positive integer, indicating the pedigree size limit for using sparse arrays (as implemented by the slam package) instead of ordinary arrays.
simplify	Simplify the output (to a numeric of length 9) if ids has length 2. Default: TRUE.
self	A logical indicating if self-relationships (i.e., between a pedigree member and itself) should be included. FALSE by default.
verbose	A logical

Details

The implementation is a modified version of Karigl's recursive algorithm (1981).

Value

If ids has length 2 and simplify = TRUE: A vector of length 9, containing the condensed identity coefficients.

Otherwise, a data frame with 11 columns and one row for each pair of individuals. The first two columns contain the ID labels, and columns 3-11 contain the condensed identity coefficients.

References

G. Karigl (1981). A recursive algorithm for the calculation of identity coefficients. Annals of Human Genetics, vol. 45.

See Also

kappa(), identityCoefs(), pedtools::founderInbreeding()

Examples

# One generation of full sib mating.
# (One of the simplest examples with all 9 coefficients nonzero.)
x = fullSibMating(1)
j1 = condensedIdentity(x, ids = 5:6)

stopifnot(all.equal(j1, c(2, 1,4, 1, 4, 1, 7, 10, 2)/32))

# Recalculate the coefficients when the founders are 100% inbred
founderInbreeding(x, 1:2) = 1
condensedIdentity(x, ids = 5:6)

---

Identity coefficients on X

Description

Computes the X chromosomal condensed identity coefficients of a pairwise relationship.

Usage

condensedIdentityX(x, ids, sparse = NA, simplify = TRUE, verbose = FALSE)

Arguments

x	A pedigree in the form of a pedtools::ped object
ids	A character (or coercible to character) containing ID labels of two or more pedigree members.
sparse	A positive integer, indicating the pedigree size limit for using sparse arrays (as implemented by the slam package) instead of ordinary arrays.
simplify	Simplify the output (to a numeric of length 9) if ids has length 2. Default: TRUE.
verbose	A logical

Details

The implementation is inspired by Karigl's recursive algorithm (1981) for the autosomal case, modified to account for X-linked inheritance.

The X chromosomal pairwise identity states depend on the sexes of the two individuals. If both are female, the states are the same as in the autosomal case. When males are involved, the two individuals have less than 4 alleles, hence the states differ from the autosomal ones. However, to avoid drawing (and learning) new pictures we re-use the autosomal states by using the following simple rule: Replace any hemizygous male allele with a pair of autozygous alleles. In this way each X state corresponds to a unique autosomal state.

For simplicity the output always contains 9 coefficients, but with NA's in the positions of undefined states (depending on the sex combination). The README file on the GitHub home page of ribd has a table illustrating this.

Value

If ids has length 2 and simplify = TRUE: A vector of length 9, containing the condensed identity coefficients. If any of the individuals are male, certain states are undefined, and the corresponding coefficients are NA. (See Details.)

Otherwise, a data frame with 11 columns and one row for each pair of individuals. The first two columns contain the ID labels, and columns 3-11 contain the condensed identity coefficients.

See Also

kinship(), identityCoefs(), pedtools::founderInbreeding()

Examples

x = fullSibMating(1)
x_sisters = swapSex(x, 5)
x_brothers = swapSex(x, 6)

condensedIdentityX(x, ids = 5:6)
condensedIdentityX(x_sisters, ids = 5:6)
condensedIdentityX(x_brothers, ids = 5:6)

---

Pedigree construction

Description

Construct a pedigree yielding a prescribed set of IBD coefficients.

Usage

constructPedigree(kappa, describe = TRUE, verbose = FALSE)

Arguments

kappa	A probability vector of length 3; $(kappa0, kappa1, kappa2)$.
describe	A logical. If TRUE, a textual description of the resulting relationship is printed.
verbose	A logical. If TRUE, various details about the calculations are printed.

Details

The construction follows the method and formulae given in Vigeland (2020).

Value

A ped object containing a pair of double half cousins with inbred founders. (In corner cases the relationship collapses into siblings.)

References

M. D. Vigeland (2020). Relatedness coefficients in pedigrees with inbred founders. Journal of mathematical biology. doi:10.1007/s00285-020-01505-x

Examples

# Full siblings
x = constructPedigree(kappa = c(0.25, 0.5, 0.25))
kappaIBD(x, leaves(x))

# A relationship halfway between parent-child and full sibs
kap = c(1/8, 6/8, 1/8)
showInTriangle(kap, label = " (1/8, 1/8)", pos = 4)

y = constructPedigree(kappa = kap)
plot(y)

stopifnot(all.equal(kappaIBD(y, leaves(y)), kap))

# kappa = (0,1,0) does not give a parent-child relationship,
# but half siblings whose shared parent is completely inbred.
z = constructPedigree(kappa = c(0,1,0))
plot(z)

---

Expected LR of a pairwise kinship test

Description

Calculates the exact likelihood ratio of a pairwise kinship test, implementing formulas of Egeland & Slooten (2016).

Usage

ELR(x, true = x, ids = leaves(x), L1, L2 = NULL, rho = NULL)

Arguments

x	An hypothesised pedigree connecting two individuals.
true	The true relationship between the two individuals.
ids	A vector containing the names of the two individuals. Note: These must occur in both x and true.
L1	The number of alleles at the first locus.
L2	The number of alleles at the second locus, or NULL (default).
rho	(If L2 is not NULL.) A numeric vector of recombination fractions. Values outside the interval $[0, 0.5]$ will raise an error.

Value

A single number, the expected LR.

References

Egeland, T. and Slooten, K. (2016). The likelihood ratio as a random variable for linked markers in kinship analysis. Int J Legal Med.

Examples

#############################
# Fig. 2 of Egeland & Slooten
#############################

rhos = seq(0, 0.5, length = 11)

dat = cbind(
  Grand = ELR(linearPed(2), ids = c(1,5), L1 = 10, L2 = 30, rho = rhos),
  Half = ELR(halfSibPed(), ids = c(4,5), L1 = 10, L2 = 30, rho = rhos),
  Uncle = ELR(avuncularPed(), ids = c(3,6), L1 = 10, L2 = 30, rho = rhos))

matplot(rhos, dat, type = "l",  lwd = 2, ylab = "E[LR]", ylim = c(0, 8))
legend("bottomleft", legend = colnames(dat), lty = 1:3, col = 1:3, lwd = 2)

---

Relatedness coefficients by other programs

Description

Wrappers for functions in other packages or external programs.

Usage

kinship2_kinship(x, ids = NULL, Xchrom = FALSE)

kinship2_inbreeding(x, Xchrom = FALSE)

Arguments

x	A pedigree, in the form of a pedtools::ped object.
ids	A integer vector of length 2.
Xchrom	A logical, indicating if the autosomal (default) or X-chromosomal coefficients should be computed.

Details

kinship2_kinship() and kinship2_inbreeding() both wrap kinship2::kinship().

Value

For kinship2_inbreeding(), a numerical vector with inbreeding coefficients, named with ID labels.

For kinship2_kinship(), either a single numeric (if ids is a pair of pedigree members) or the whole kinship matrix, with the ID labels as dimnames.

See Also

kinship2::kinship()

Examples

# A random pedigree with 7 individuals
p = randomPed(n = 7, seed = 123)

### Kinship matrix

# Autosomal: Check that ribd agrees with kinship2
stopifnot(identical(
  kinship(p),          # ribd
  kinship2_kinship(p)  # kinship2
))

# X chromosomal kinship
stopifnot(identical(
  kinship(p, Xchrom = TRUE),          # ribd
  kinship2_kinship(p, Xchrom = TRUE)  # kinship2
))


### Inbreeding coefficients

# Autosomal
stopifnot(identical(
  inbreeding(p),          # ribd
  kinship2_inbreeding(p)  # kinship2
))

# X chromosomal
stopifnot(identical(
  inbreeding(p, Xchrom = TRUE),          # ribd
  kinship2_inbreeding(p, Xchrom = TRUE)  # kinship2
))

---

Generalised kinship coefficients

Description

Computes single-locus generalised kinship coefficients of various kinds. These are fundamental for computing identity coefficients (see identityCoefs()), but are also interesting in their own right. Each generalised kinship coefficient is defined as the probability of observing a corresponding generalised IBD pattern, as defined and discussed in the Details section below.

Usage

gKinship(
  x,
  pattern,
  distinct = TRUE,
  Xchrom = FALSE,
  method = c("auto", "K", "WL", "LS", "GC"),
  verbose = FALSE,
  debug = FALSE,
  mem = NULL,
  ...
)

gip(x, pattern, distinct = TRUE)

Arguments

x	A ped object.
pattern	A gip object, or a list of vectors to be passed onto gip(). Each vector should contain members of x constituting an IBD block. (See Details and Examples.)
distinct	A logical indicating if different blocks are required to be non-IBD. Default: TRUE. (Irrelevant for single-block patterns.)
Xchrom	A logical, by default FALSE.
method	Either "auto", "K", "WL", "LS" or "GC".
verbose	A logical, by default FALSE.
debug	A logical, by default FALSE.
mem	For internal use.
...	Further arguments.

Details

The starting point: standard kinship coefficients

The classical kinship coefficient phi between two pedigree members A and B, is the probability that two alleles sampled from A and B (one from each), at a random autosomal locus, are identical by descent (IBD).

In the language and notation to be introduced shortly, we would write ⁠phi = Pr[(A,B)]⁠ where ⁠(A,B)⁠ is an IBD pattern.

Generalised IBD patterns

We define a generalised IBD pattern (GIP) to be a partition of a set of alleles drawn from members of a pedigree, such that the alleles in each subset are IBD. Each subset (also referred to as a group or a block) is written as a collection of pedigree members (A, B, ...), with the understanding that each member represents one of its alleles at the given locus. A member may occur in multiple blocks, and also more than once within a block.

Additional requirements give rise to different flavours of GIPs (and their corresponding coefficients):

• Distinct (resp. non-distinct): alleles in different blocks are non-IBD (resp. may be IBD)

• Deterministic (resp. random): the parental origin (paternal or maternal) of each allele is fixed (resp. unknown).

We may say that a GIP is partially (rather than fully) deterministic if the parental origin is fixed for some, but not all alleles involved.

Notational examples

Our notation distinguishes the different types of patterns, as exemplified below. Blocks are separated with "/" if they are distinct, and "&" otherwise. Deterministically sampled alleles are suffixed by either ":p" (paternal) or ":m" (maternal).

• ⁠(A, B) & (A, C)⁠: 4 alleles are sampled randomly; two from A, one from B and one from C. The first from A is IBD with that from B, and the second from A is IBD with that from C. All four alleles may be IBD. [Random, non-distinct]

• ⁠(A, B) / (A, C)⁠: Same as the previous, but the two allele pairs must be non-IBD. [Random, distinct]

• ⁠(A:p, C:p) / (C:m)⁠: The paternal alleles of A and C are IBD, and different from the maternal allele of C. [Deterministic, distinct]

• ⁠(A, C:p) & (B, C:m)⁠: The paternal and maternal alleles of C are IBD with random alleles of from A and B, respectively. The two pairs are not necessarily different. [Partially deterministic, non-distinct]

• ⁠(A:p, A, A)⁠: Here we have just one group, specifying that the paternal allele of A is IBD with two other alleles sampled randomly from A. (If A is non-inbred, this must have probability 1/4.) [Partially deterministic, single-block]

In the gip() constructor, deterministic sampling is indicated by naming elements with "p" or "m", e.g., c(p = A) produces (A:p). See Examples for how to create the example patterns listed above.

Internal structure of gip objects

(Note: This section is included only for completeness; gip objects should not be directly manipulated by end users.)

Internally, a GIP is stored as a list of integer vectors, each vector giving the indices of pedigree members constituting an IBD block. In addition, the object has three attributes:

• labs: A character vector containing the names of all pedigree members

• deterministic: A logical, which is TRUE if the pattern is (partially or fully) deterministic

• distinct: A logical.

If deterministic = TRUE, the last digit of each integer encodes the parental origin of the allele (0 = unknown; 1 = paternal; 2 = maternal). For example:

• 12 = the maternal origin of individual 1

• 231 = the paternal allele of individual 23

• 30 = a random allele of individual 3

A brief history of generalised kinship coefficients

The notion of generalised kinship coefficients originated with Karigl (1981) who used a selection of random, non-distinct patterns (in our terminology) to compute identity coefficients.

Weeks & Lange (1988), building on Karigl's work, defined random, distinct patterns in full generality and gave an algorithm for computing the corresponding coefficients.

In a follow-up paper, Lange & Sinsheimer (1992) introduced partially deterministic (distinct) patterns, and used these to compute detailed identity coefficients.

In another follow-up, Weeks et al. (1995) extended the work on random, distinct patterns by Weeks & Lange (1988) to X-chromosomal loci.

Garcia-Cortes (2015) gave an alternative algorithm for the detailed identity coefficients, based on (in our terminology) fully deterministic, non-distinct patterns.

Implemented algorithms

The following are valid options for the methods parameters, and what they implement.

• auto: Chooses method automatically, based on the pattern type.

• K: Karigl's algorithm for random, non-distinct patterns. Only the cases considered by Karigl are currently supported, namely single groups up to length 4, and two groups of length two. The implementation in ribd includes an X-chromosomal version, and allows inbred founders.

• WL: Weeks & Lange's algorithm for random, distinct patterns of any size. [TODO: Include the extension to X by Weeks et al. (1995).]

• LS: Lange & Sinsheimer's algorithm for partially deterministic, distinct patterns of any size. Does not support X, nor patterns involving inbred founders.

• GC: Garcia-Cortes' algorithm for fully deterministic, non-distinct patterns. The current implementation only covers the patterns needed to compute identity coefficients, namely single blocks and two blocks of length two. The original algorithm has been extended to an X-chromosomal version, and to pedigrees with inbred founders.

Value

gKinship() returns a single number, the probability of the given IBD pattern.

gip() returns an object of class gip. This is internally a list of integer vectors, with attributes labs, deterministic and distinct. (See also Details.)

References

• G. Karigl (1981). A recursive algorithm for the calculation of identity coefficients. Ann. Hum. Genet.

• D.E. Weeks & K. Lange (1988). The affected-pedigree-member method of linkage analysis. Am. J. Hum. Genet

• K. Lange & J.S. Sinsheimer (1992). Calculation of genetic identity coefficients. Ann. Hum. Genet.

• D.E. Weeks, T.I. Valappil, M. Schroeder, D.L. Brown (1995) An X-linked version of the affected-pedigree-member method of linkage analysis. Hum Hered.

• L.A. García-Cortés (2015). A novel recursive algorithm for the calculation of the detailed identity coefficients. Gen Sel Evol.

See Also

kinship(), identityCoefs()

Examples

### Trivial examples ###

x = nuclearPed(father = "A", mother = "B", children = "C")

# Random, distinct
patt1 = gip(x, list(c("A", "B"), c("A", "C")))
patt1

# Random, non-distinct
patt2 = gip(x, list(c("A", "B"), c("A", "C")), distinct = FALSE)
patt2

# Fully deterministic, distinct
patt3 = gip(x, list(c(p="A", p="C"), c(m="C")))
patt3

# Partially deterministic, non-distinct`
patt4 = gip(x, list(c("A", p="C"), c("B", m="C")), distinct = FALSE)
patt4

# Partially deterministic, single block
patt5 = gip(x, list(c(p="A", "A", "A")))
patt5

stopifnot(
  gKinship(x, patt1) == 0,      # (since A and B are unrelated)
  gKinship(x, patt2) == 0,      # (same as previous)
  gKinship(x, patt3) == 0.5,    # (only uncertainty is which allele A gave to C)
  gKinship(x, patt4) == 0.25,   # (distinct irrelevant)
  gKinship(x, patt5) == 0.25   # (both random must hit the paternal)
)



### Kappa coefficients via generalised kinship ###

# NB: Much less efficient than `kappaIBD()`; only for validation

kappa_from_gk = function(x, ids, method = "WL") {
  fa1 = father(x, ids[1])
  fa2 = father(x, ids[2])
  mo1 = mother(x, ids[1])
  mo2 = mother(x, ids[2])

  GK = function(...) gKinship(x, list(...), method = method)

  k0 = GK(fa1, fa2, mo1, mo2)
  k1 = GK(c(fa1, fa2), mo1, mo2) + GK(c(fa1, mo2), fa2, mo1) +
       GK(c(mo1, fa2), fa1, mo2) + GK(c(mo1, mo2), fa1, fa2)
  k2 = GK(c(fa1, fa2), c(mo1, mo2)) + GK(c(fa1, mo2), c(mo1, fa2))
  c(k0, k1, k2)
}

y1 = nuclearPed(2); ids = 3:4
stopifnot(kappa_from_gk(y1, ids) == kappaIBD(y1, ids))

y2 = quadHalfFirstCousins(); ids = 9:10
stopifnot(kappa_from_gk(y2, ids) == kappaIBD(y2, ids))


### Detailed outputs and debugging ###

x = fullSibMating(1)

# Probability of sampling IBD alleles from 1, 5 and 6
p1 = gip(x, list(c(1,5,6)))
p1
gKinship(x, p1, method = "K", verbose = TRUE, debug = TRUE)
gKinship(x, p1, method = "WL", verbose = TRUE, debug = TRUE)

# Probability that paternal of 5 is IBD with maternal of 6
p2 = gip(x, list(c(p=5, m=6)))
p2
gKinship(x, p2, method = "LS", verbose = TRUE, debug = TRUE)
gKinship(x, p2, method = "GC", verbose = TRUE, debug = TRUE)

# Probability that paternal of 5 is *not* IBD with maternal of 6
p3 = gip(x, list(c(p=5), c(m=6)), distinct = TRUE)
p3
gKinship(x, p3, method = "LS", verbose = TRUE, debug = TRUE)

---

Colourised IBD plot

Description

This is a pedagogical tool for illustrating the concept of identity-by-descent, by representing the alleles in a pedigree by coloured points or letters. By default, the alleles are placed below each pedigree symbol, but this may be modified. (See examples.)

Usage

ibdDraw(
  x,
  alleles,
  symbol = c("point", "text"),
  pos = 1,
  cols = NULL,
  cex = NA,
  sep = 1,
  dist = 1,
  labs = FALSE,
  checkFounders = TRUE,
  checkParents = TRUE,
  ...
)

Arguments

x	A ped object.
alleles	A list of length pedsize(x). Each element should consist of one or two integers, representing different colours. Zeroes produce "greyed-out" alleles.
symbol	Either "point" or "text".
pos	A vector recycled to the length of labels(x), indicating allele placement relative to the pedigree symbols: 0 = inside; 1 = below; 2 = left; 3 = above; 4 = right. By default, all are placed below.
cols	A colour vector corresponding to the integers occurring in alleles.
cex	An expansion factor for the allele points/letters. Default: 3 for points and 2 for text.
sep	The separation between alleles within a pair, given as a multiple of the width of a pedigree symbol. Default is 1 when pos > 0 and 0.5 for pos = 0.
dist	The distance between pedigree symbols and the alleles, given as a multiple of symbol size. Default: 1. Ignored when pos = 0.
labs	A logical indicating if labels should be included.
checkFounders	A logical. If TRUE (default), a warning is issued if a founder has two equal alleles other than 0.
checkParents	A logical. If TRUE (default), a warning is issued if someone's alleles don't match those of the parents. This a superficial test and does not catch all Mendelian errors.
...	Further arguments passed on to plot.ped().

Value

The plot structure is returned invisibly.

See Also

pedtools::plot.ped(), ibdsim2::haploDraw()

Examples

op = par(no.readonly = TRUE)

###############################
# Example 1: A family quartet #
###############################

x = nuclearPed(2)
als = list(1:2, 3:4, c(1,3), c(2,3))

# Default options
ibdDraw(x, als)

# Nicer colors
cols = c(7, 3, 2, 4)
ibdDraw(x, als, cols = cols)

# Inside the pedigree symbols
ibdDraw(x, als, cols = cols, pos = 0, symbolsize = 2.5)

# Other placements
ibdDraw(x, als, cols = cols, pos = c(2, 3, 1, 4))

# Letters instead of points
ibdDraw(x, als, cols = cols, symbol = "text")

# Further arguments (note that `col` is an argument of `ped.plot()`)
ibdDraw(x, als, cols = cols, pos = 0, symbolsize = 2.5,
        labs = TRUE, fill = "lightgray")

# Mutations are warned about (unless `checkParents = FALSE`)
ibdDraw(x, alleles = list(1:2, 3:4, 5, 6))


##############################
# Example 2: Cousin pedigree #
##############################

x = cousinPed(1) |> swapSex(3) |> relabel()
als = list(1:2, 3:4, NULL, c(1,3), c(2,3), NULL, 3, 3)

cols = c(7, 3, 2, 4)
ibdDraw(x, als, cols = cols, dist = 0.8)
ibdDraw(x, als, cols = cols, dist = 0.8, symbol = "text")

# Alternative: 0's give greyed-out alleles
als2 = list(1:2, 3:4, c(0,0), c(1,3), c(2,3), c(0,0), c(0,3), c(3,0))

ibdDraw(x, als2, cols = cols, dist = 0.8)
ibdDraw(x, als2, cols = cols, dist = 0.8, symbol = "text")


############################
# Example 3: X inheritance #
############################

x = nuclearPed(2, sex = c(1, 2))
als = list(1, 2:3, 3, c(1, 3))
ibdDraw(x, als, cols = c(3, 7, 2))


#################################
# Example 4: mtDNA inheritance  #
#################################

x = linearPed(2, sex = 2)
als = list(1, 2, 3, 2, 2)
ibdDraw(x, als, cols = 2:4)


# Restore graphics parameters
par(op)

---

IBD triangle plot

Description

A relationship triangle used to used to visualize the kappa coefficients of between non-inbred individuals. Various annotations are available, including points marking the most common relationships, contour lines for the kinship coefficients, and shading of the unattainable region. The companion function showInTriangle() (which plots user-specified points onto the triangle) is probably the most useful for end users.

Usage

ibdTriangle(
  relationships = c("UN", "PO", "MZ", "S", "H,U,G", "FC"),
  plotType = c("base", "ggplot2", "plotly"),
  pch = 19,
  cexPoint = 1.2,
  cexText = 1.2,
  cexAxis = cexText,
  kinshipLines = numeric(),
  shortLines = FALSE,
  shading = "gray90",
  xlim = c(0, 1),
  ylim = c(0, 1),
  axes = FALSE,
  las = 1,
  xlab = expression(kappa[0]),
  ylab = expression(kappa[2]),
  title = NULL,
  mar = c(2.1, 2.1, 1, 1),
  xpd = TRUE,
  keep.par = TRUE,
  cexLab = NULL,
  ...
)

Arguments

relationships	A character vector indicating the fixed relationships points to be included in the plot. Valid entries are those in the label column of basicRelationships.
plotType	Either "base" (default), "ggplot2" or "plotly". Abbreviations are allowed.
pch	Symbol used for the relationship points (see par()).
cexPoint	A number controlling the symbol size for the relationship points.
cexText	A number controlling the font size for the relationship labels.
cexAxis	A number controlling the font size for the axis labels.
kinshipLines	A numeric vector (see Details).
shortLines	A logical indicating if the kinship lines (if present) should be restricted to the interior of the triangle.
shading	The shading colour for the unattainable region.
xlim, ylim, xpd, las	Graphical parameters; see par(). (Base plot only.)
axes	A logical: Draw surrounding axis box? Default: FALSE.
xlab, ylab	Axis labels.
title	Main title (absent by default).
mar	Graphical parameter; see par(). For ggplot2, this is ignored unless it is a ggplot2::margin() object.
keep.par	A logical. If TRUE, the graphical parameters are not reset after plotting, which may be useful for adding additional annotation. (Base plot only.)
cexLab	Deprecated; use cexAxis instead.
...	Further arguments; currently not used.

Details

For any pair of non-inbred individuals A and B, their genetic relationship can be summarized by the IBD coefficients $(\kappa_0, \kappa_1, \kappa_2)$, where $\kappa_i$ = P(A and B share i alleles IBD at random autosomal locus). Since $\kappa_0 + \kappa_1 + \kappa_2 = 1$, any relationship corresponds to a point in the triangle in the $(\kappa_0, \kappa_2)$-plane defined by $\kappa_0 \ge 0, \kappa_2 \ge 0, \kappa_0 + \kappa_2 \le 1$. The choice of $\kappa_0$ and $\kappa_2$ as the axis variables is done for reasons of symmetry and is not significant (other authors have used different views of the triangle).

As shown by Thompson (1976), points in the subset of the triangle defined by $4\kappa_0\kappa_2 > \kappa_1^2$ are unattainable for pairwise relationships. By default this region in shaded in a light grey colour, but this can be modified with the shading argument.

The IBD coefficients are linearly related to the kinship coefficient $\varphi$ by the formula $\varphi = 0.25\kappa_1 + 0.5\kappa_2.$ By indicating values for $\varphi$ in the kinshipLines argument, the corresponding contour lines are shown in the triangle plot. (Currently only when plotType = "base".)

Value

NULL if plotType = 'base'; otherwise the plot object.

References

• E. A. Thompson (1975). The estimation of pairwise relationships. Annals of Human Genetics 39.

• E. A. Thompson (1976). A restriction on the space of genetic relationships. Annals of Human Genetics 40.

See Also

showInTriangle(), kappaIBD()

Examples

opar = par(no.readonly = TRUE) # store graphical parameters

ibdTriangle()
ibdTriangle(kinshipLines = c(0.25, 0.125), shading = NULL, cexText = 0.7)
ibdTriangle(kinshipLines = c(0.25, 0.125), shortLines = TRUE, pch = 15)
ibdTriangle(relationships = c("UN", "PO", "MZ", "S"),
            xlab = "k0", ylab = "k2", las = 0, axes = TRUE, cexAxis =1.6)

par(opar) # reset graphical parameters

---

Omnibus function for identity coefficients

Description

This function calculates the pairwise identity coefficients described by Jacquard (1974). Unlike the previous condensedIdentity() (which will continue to exist), this function also computes the 15 detailed identity coefficients. The implementation supports pedigrees with inbred founders, and X-chromosomal coefficients.

Usage

identityCoefs(
  x,
  ids = labels(x),
  detailed = FALSE,
  Xchrom = FALSE,
  self = FALSE,
  simplify = TRUE,
  method = c("auto", "K", "WL", "LS", "GC", "idcoefs", "identity", "merlin"),
  verbose = FALSE,
  ...
)

detailed2condensed(d)

Arguments

x	A pedigree in the form of a pedtools::ped object.
ids	A vector of two ID labels.
detailed	A logical. If FALSE (default), the 9 condensed coefficients are computed; otherwise the 15 detailed identity coefficients.
Xchrom	A logical, by default FALSE.
self	A logical indicating if self-relationships (i.e., between a pedigree member and itself) should be included. FALSE by default.
simplify	Simplify the output (to a numeric of length 9) if ids has length 2. Default: TRUE.
method	Either "auto", "K", "WL", "LS", "GC", "idcoefs", "identity" or "merlin". By default ("auto") a suitable algorithm is chosen automatically.
verbose	A logical.
...	Further arguments.
d	Either a numeric vector of length 15, or a data frame with 17 columns.

Details

Both the condensed and detailed coefficients are given in the orders used by Jacquard (1974). The function detailed2condensed() converts from detailed coefficients (d1, ..., d15) to condensed ones (D1, ..., D9) using the following relations:

• D1 = d1

• D2 = d6

• D3 = d2 + d3

• D4 = d7

• D5 = d4 + d5

• D6 = d8

• D7 = d9 + d12

• D8 = d10 + d11 + d13 + d14

• D9 = d15

Algorithms for computing identity coefficients

The following is a brief overview of various algorithms for computing (single-locus) condensed and/or detailed identity coefficients. This topic is closely linked to that of generalised kinship coefficients, which is further described in the documentation of gKinship().

For each algorithm below, it is indicated in brackets how to enforce it in identityCoefs().

• Karigl (1981) gave the first recursive algorithm for the 9 condensed identity coefficients. [method = "K"]

• Weeks & Lange (1988) suggested a broader and more natural generalisation of kinship coefficients, leading to a slightly different algorithm for condensed coefficients. [method = "WL"]

• Lange & Sinsheimer (1992) described an even further generalisation of kinship coefficients, allowing a mix of deterministic and random sampling of alleles. They used this to give (i) an alternative algorithm for the 9 condensed identity coefficients, and (ii) an algorithm for the 15 detailed coefficients. [method = "LS"]

• The C program IdCoefs (version 2.1.1) by Mark Abney (2009) uses a graph model to obtain very fast computation of condensed identity coefficients. This requires IdCoefs to be installed on the computer (see link under References) and available on the system search path. The function then writes the necessary files to disk and calls IdCoefs via system(). [method = "idcoefs"]

• The R package identity provides an R interface for IdCoefs, avoiding calls to system(). [method = "identity"]

• The MERLIN software (Abecasis et al, 2002) offers an option "–extended" for computing detailed identity coefficients. This option requires MERLIN to be installed on the system. The function then writes the necessary files to disk and calls MERLIN via system(). If detailed = FALSE, the coefficients are transformed with detailed2condensed() before returning. Note: MERLIN rounds all numbers to 3 decimal places. Since this rounding is done on the detailed coefficients, rounding errors may happen when converting to the condensed ones. [method = "merlin"]

Value

A data frame with L + 2 columns, where L is either 9 or 15 (if detailed = TRUE).

If simplify = TRUE and length(ids) = 2: A numeric vector of length L.

References

• Jacquard, A. (1974). The Genetic Structure of Populations. Springer.

• Karigl, G. (1981). A recursive algorithm for the calculation of identity coefficients. Ann. Hum. Genet.

• Weeks, D.E. & Lange, K. (1988). The affected-pedigree-member method of linkage analysis. Am. J. Hum. Genet

• Lange, K. & Sinsheimer, J.s. (1992). Calculation of genetic identity coefficients. Ann. Hum. Genet.

• Abney, M. (2009). A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients. Bioinformatics, 25, 1561-1563. https://home.uchicago.edu/~abney/abney_web/Software.html

See Also

condensedIdentity(), gKinship()

Examples

x = fullSibMating(1)

### Condensed coefficients
j1 = identityCoefs(x, method = "K")
j2 = identityCoefs(x, method = "WL")
j3 = identityCoefs(x, method = "LS")
j4 = identityCoefs(x, method = "GC")
j5 = condensedIdentity(x, ids = 1:6) # legacy version

stopifnot(all.equal(j1,j2), all.equal(j1,j3), all.equal(j1,j4), all.equal(j1,j5))

### Detailed coefficients
jdet1 = identityCoefs(x, detailed = TRUE, method = "LS")
jdet2 = identityCoefs(x, detailed = TRUE, method = "GC")

stopifnot(all.equal(jdet1,jdet2))

### X-chromosomal coefficients
jx1 = identityCoefs(x, Xchrom = TRUE, method = "K")
jx2 = identityCoefs(x, Xchrom = TRUE, method = "GC")
jx3 = condensedIdentityX(x, ids = 1:6)  # legacy version

stopifnot(all.equal(jx1,jx2), all.equal(jx1,jx3))

### Detailed X-chromosomal coefficients
jdx = identityCoefs(x, detailed = TRUE, Xchrom = TRUE, method = "GC")

stopifnot(all.equal(detailed2condensed(jdx), jx1))

---

Inbreeding coefficients

Description

Compute the inbreeding coefficients of all members of a pedigree. Both autosomal and X-chromosomal coefficients are supported. This function is a simple wrapper of kinship(). Note that pedigree founders are allowed to be inbred; see pedtools::founderInbreeding() for how to set this up, and see Examples below.

Usage

inbreeding(x, ids = NULL, Xchrom = FALSE)

Arguments

x	A pedigree in the form of a ped object, or a list of such.
ids	A vector of ID labels, or NULL (default).
Xchrom	A logical, indicating if the autosomal (default) or X-chromosomal inbreeding coefficients should be computed.

Details

The autosomal inbreeding coefficient of a pedigree member is defined as the probability that, at a random autosomal locus, the two alleles carried by the member are identical by descent relative to the pedigree. It follows from the definition that the inbreeding coefficient of a non-founder equals the kinship coefficient of the parents.

The implementation here uses kinship() to compute the kinship matrix, and computes the inbreeding coefficients from the diagonal, by the formula

$f_a = 2*\phi_{aa} - 1.$

The X chromosomal inbreeding coefficient of females are defined (and computed) similarly to the autosomal case above. For males is it always defined as 1.

Value

If ids has length 1, the inbreeding coefficient of this individual is returned as a single unnamed number.

Otherwise, the output is a named numeric vector containing the inbreeding coefficients of the indicated pedigree members (if ids = NULL: all).

See Also

kinship()

Examples

# Child of half siblings: f = 1/8
x = halfCousinPed(0, child = TRUE)

# Inbreeding vector
inbreeding(x)

# Simpler output using the `ids` argument:
inbreeding(x, ids = 6)


### X-chromosomal inbreeding ###

# Males have inbreeding coefficient 1
stopifnot(inbreeding(x, ids = 6, Xchrom = TRUE) == 1)

y1 = swapSex(x, ids = 6)  # female child
stopifnot(inbreeding(y1, ids = 6, Xchrom = TRUE) == 0)

y2 = swapSex(y1, ids = 2) # female ancestor
stopifnot(inbreeding(y2, ids = 6, Xchrom = TRUE) == 0.25)


### Inbred founder ###

# Mother 100% inbred
founderInbreeding(x, ids = 2) = 1

inbreeding(x)


# Example with selfing and complete inbreeding
s = selfingPed(1)
founderInbreeding(s, 1) = 1
stopifnot(inbreeding(s, ids = 2) == 1)

---

Jicaque pedigree

Description

A data frame describing a pedigree from the Jicaque tribe, studied by Chapman and Jacquard (1971).

Usage

jicaque

Format

A data frame with 22 rows and four columns:

• id : individual ID

• fid : father's ID (or 0 if not included)

• mid : mother's ID (or 0 if not included)

• sex : Gender codes, where 1 = male and 2 = female

References

Chapman, A.M and Jacquard, A. (1971). Un isolat d'Amerique Centrale: les Indiens Jicaques de Honduras. In Genetique et Population. Paris: Presses Universitaires de France.

---

IBD (kappa) coefficients

Description

Computes the three IBD coefficients summarising the relationship between two non-inbred individuals. Both autosomal and X chromosomal versions are implemented. The pedigree founders (other than the individuals in question) are allowed to be inbred; see pedtools::founderInbreeding() for how to set this up, and see Examples below.

Usage

kappaIBD(
  x,
  ids = labels(x),
  inbredAction = 1,
  simplify = TRUE,
  acrossComps = TRUE,
  Xchrom = FALSE
)

Arguments

x	A pedigree in the form of a ped object (or a list of such).
ids	A character (or coercible to character) containing ID labels of two or more pedigree members.
inbredAction	An integer telling the program what to do if either of the ids individuals are inbred. Possible values are: 0 = do nothing; 1 = print a warning message (default); 2 = raise an error. In the first two cases the coefficients are reported as NA.
simplify	Simplify the output (to a numeric of length 3) if ids has length 2. Default: TRUE.
acrossComps	A logical indicating if pairs of individuals in different components should be included. Default: TRUE.
Xchrom	A logical, indicating if the autosomal (default) or X-chromosomal kappa coefficients should be computed.

Details

For non-inbred individuals a and b, their autosomal IBD coefficients $(\kappa_0, \kappa_1, \kappa_2)$ are defined as follows:

$\kappa_i = P(\text{a and b share exactly i alleles IBD at a random autosomal locus})$

The autosomal kappa coefficients are computed from the kinship coefficients. When a and b are both nonfounders, the following formulas hold:

• $\kappa_2 = \varphi_{MM} \cdot \varphi_{FF} + \varphi_{MF} \cdot\varphi_{FM}$

• $\kappa_1 = 4 \varphi_{ab} - 2 \kappa_2$

• $\kappa_0 = 1 - \kappa_1 - \kappa_2$

Here $\varphi_{MF}$ denotes the kinship coefficient between the mother of a and the father of b, etc. If either a or b is a founder, then $\kappa_2 = 0$, while the other two formulas remain as before.

The X-chromosomal IBD coefficients are defined similarly to the autosomal case. Here $\kappa_2$ is undefined when one or both individuals are male, which greatly simplifies the calculations when males are involved. The formulas are (with $\varphi_{ab}$ now referring to the X-chromosomal kinship coefficient):

• Both male: $(\kappa_0, \kappa_1, \kappa_2) = (1-\varphi_{ab}, \varphi_{ab}, \text{NA})$

• One male, one female: $(\kappa_0, \kappa_1, \kappa_2) = (1-2 \varphi_{ab}, 2 \varphi_{ab}, \text{NA})$

• Two females: Similar formulas as in the autosomal case.

Value

If ids has length 2 and simplify = TRUE: A numeric vector of length 3: $(\kappa_0, \kappa_1, \kappa_2)$.

Otherwise: A data frame with one row for each pair of individuals, and 5 columns. The first two columns contain the ID labels, and columns 3-5 contain the IBD coefficients.

Kappa coefficients of inbred individuals (meaning X-inbred females if Xchrom = T) are reported as NA, unless inbredAction = 2.

The X-chromosomal $\kappa_2$ is NA whenever at least one of the two individuals is male.

See Also

kinship(), identityCoefs() for coefficients allowing inbreeding, showInTriangle() for plotting kappa coefficients in the IBD triangle.

Examples

### Siblings
x = nuclearPed(2)
kappaIBD(x)

k = kappaIBD(x, 3:4)
stopifnot(identical(k, c(.25, .5, .25)))

### Quad half first cousins
x = quadHalfFirstCousins()
k = kappaIBD(x, ids = leaves(x))
stopifnot(identical(k, c(17/32, 14/32, 1/32)))

### Paternal half brothers with 100% inbred father
# Genetically indistinguishable from an (outbred) father-son relationship
x = halfSibPed() |> setFounderInbreeding(ids = 2, value = 1)
plot(x, hatched = 4:5)

k = kappaIBD(x, 4:5)
stopifnot(identical(k, c(0, 1, 0)))

### X-chromosomal kappa
y = nuclearPed(2, sex = 2)
kappaIBD(y, Xchrom = TRUE)

---

Degree of relationship

Description

Converts a vector of kinship coefficients to "degrees of relationship", as used by some software for relatedness inference (e.g. KING).

Usage

kin2deg(kin, unrelated = Inf)

Arguments

kin	A vector of kinship coefficients, i.e., numbers in ⁠[0, 1]⁠.
unrelated	The conversion of unrelated individuals (kin = 0). Mathematically this corresponds to degree = Inf, but in some situations degree = NA or something else might be preferable.

Details

The implementation uses the conversion formula

$deg = round(-log2(kin) - 1).$

The first degrees correspond to the following approximate kinship ranges:

• ⁠[0.354, 1]⁠: 0th degree (MZ twins or duplicates)

• ⁠[0.177, 0.354)⁠: 1st degree (parent-offspring, full siblings)

• ⁠[0.0884, 0.177)⁠: 2nd degree (half sibs, grandparent-grandchild, avuncular)

• ⁠[0.0442, 0.0884)⁠ 3rd degree (half-avuncular, first cousins, great-grandparent etc)

Value

An integer vector of the same length as kin.

References

KING manual with thresholds for relationship degrees: https://www.kingrelatedness.com/manual.shtml

See Also

kinship(), coeffTable()

Examples

x = cousinPed(1)

# Kinship matrix
k = kinship(x)

# Degrees
deg = kin2deg(k)
deg

# First cousins are 3rd degree
stopifnot(deg['7', '8'] == 3)

---

Kinship coefficients

Description

Compute the matrix of pairwise kinship coefficients in a pedigree. Both autosomal and X-chromosomal versions are supported. The pedigree founders are allowed to be inbred; see pedtools::founderInbreeding() for how to set this up, and see Examples below.

Usage

kinship(x, ids = NULL, simplify = TRUE, Xchrom = FALSE)

Arguments

x	A ped object or a list of such.
ids	Either NULL (default), or a vector of ID labels in x.
simplify	A logical. by default TRUE. See Value.
Xchrom	A logical, indicating if the autosomal (default) or X-chromosomal kinship coefficients should be computed.

Details

For two (possibly equal) members A, B of a pedigree, their autosomal (resp. X-chromosomal) kinship coefficient is defined as the probability that a random allele from A and a random allele from B, sampled at the same autosomal (resp. X-chromosomal) locus, are identical by descent relative to the pedigree.

Value

A symmetric N * N matrix, where N is the number of pedigree members, or length(ids) if this is given, containing the pairwise kinship coefficients. If ids has length 2, and simplify = TRUE, the function returns a single number.

See Also

inbreeding(), kappa()

Examples

# Kinship coefficients in a nuclear family with two children
x = nuclearPed(2)
kinship(x)

# X chromosomal kinship coefficients in the same family
kinship(x, Xchrom = TRUE)

# Autosomal kinships if the mother is 100% inbred
founderInbreeding(x, 2) = 1
kinship(x)

# Similar for X:
founderInbreeding(x, 2, chromType = "X") = 1
kinship(x, Xchrom = TRUE)

---

Minimal IBD pattern

Description

Compute the minimal form of given multiperson IBD pattern.

Usage

minimalPattern(x)

Arguments

x	An integer vector of even length.

Value

An integer vector of the same length as x.

Examples

v = c(1,2,2,3)
stopifnot(identical(minimalPattern(v), c(1,2,1,3)))

---

Multi-person IBD coefficients

Description

Computes the probabilities (coefficients) of all possible patterns of identity-by-descent (IBD) sharing among N non-inbred individuals, at a single autosomal locus. The reported coefficients are "condensed" in the sense that allele ordering within each individual is ignored. For N = 2, the result should agree with the traditional "kappa" coefficients, as computed by kappaIBD(). The current implementation handles up to N = 6 individuals.

Usage

multiPersonIBD(x, ids, complete = FALSE, verbose = FALSE)

Arguments

x	A ped object.
ids	A vector of ID labels.
complete	A logical. If FALSE, only IBD patterns with nonzero probability are included in the output.
verbose	A logical. If TRUE, some computational details are printed.

Details

Consider N members of a pedigree, i1, i2, ... iN. A pattern of IBD sharing between these individuals is a sequence of N ordered pairs of labels, (a1_1, a1_2), (a2_1, a2_2), ... (aN_1, aN_2), where ai_1 and ai_2 represent the paternal and maternal allele of individual i, respectively. Equality of labels means that the corresponding alleles are IBD, and vice versa.

We say that two IBD patterns are equivalent if one can be transformed into the other by some combination of

• renaming the labels (without changing the structure)

• swapping the paternal/maternal labels of some individuals

Each equivalence class has a "minimal" element, using integer labels, and being minimal with respect to standard sorting. For example, the minimal element equivalent to ⁠(a,c),(d,c),(b,b)⁠ is ⁠(1,2),(2,3),(4,4)⁠.

Value

A data frame in which each row corresponds to an equivalence class of multi-person IBD patterns. The first column gives the calculated probability, followed by one column for each ids individual, describing the minimal element of the equivalence class. (See Details.) If complete = FALSE (the default) rows with probability 0 are removed.

Examples

### Trivial example: Trio ###
x = nuclearPed(1)
ids = 1:3
multiPersonIBD(x, ids, complete = TRUE)

### Example due to Peter Green ###
# Three (pairwise) cousins arranged in two different ways,
# with different 3-way IBD coefficients.

threeCousins1 = ped(
  id  = c('gf','gm','gf1','gf2','gf3','gm1','gm2','gm3',
          'f1','f2','f3','m1','m2','m3','c1','c2','c3'),
  fid = c(0,0,0,0,0,0,0,0,'gf1','gf2','gf3','gf','gf','gf',
          'f1','f2','f3'),
  mid = c(0,0,0,0,0,0,0,0,'gm1','gm2','gm3','gm','gm','gm',
          'm1','m2','m3'),
  sex = c(1,2,1,1,1,2,2,2,1,1,1,2,2,2,1,1,1))

threeCousins2 = ped(
  id  = c('gf1','gf2','gf3','gm1','gm2','gm3','f1','f2','f3',
          'm1','m2','m3','c1','c2','c3'),
  fid = c(0,0,0,0,0,0,'gf2','gf3','gf1','gf3','gf1','gf2',
          'f1','f2','f3'),
  mid = c(0,0,0,0,0,0,'gm2','gm3','gm1','gm3','gm1','gm2',
          'm1','m2','m3'),
  sex = c(1,1,1,2,2,2,1,1,1,2,2,2,1,1,1))

ids = c('c1','c2','c3')
multiPersonIBD(threeCousins1, ids)
multiPersonIBD(threeCousins2, ids)

---

Variance of realised relatedness coefficients

Description

Compute the variance of realised relatedness coefficients, by doubly integrating the corresponding two-locus coefficients.

Usage

realisedIbdVariance(x, ids = leaves(x), coeff, L = 1)

Arguments

x	A ped object.
ids	A vector naming two members of x.
coeff	A string naming a coefficient for which the variance is to be computed. See Details for legal values.
L	A positive number; the chromosome length in Morgan.

Details

The double integral method was used by Guo to compute the variation in proportion of the genome shared IBD (Guo 1995, see also Thompson 2013). The method extends directly to other coefficients. The implementation here supports Cotterman's kappa coefficients (of noninbred individuals), and Jacquard's condensed identity coefficients.

This function is a bare-bones implementation of the double integral method, based on stats::integrate, and can probably be optimised in various ways.

The coeff parameter must be either a character naming the coefficient to compute, or a function. If a character, it must be one of the following names:

• "inb" (inbreeding coefficient)

• "kinship", "phi" (synonyms for the kinship coefficient)

• "k0", "k1", "k2" (kappa coefficients of noninbred individuals)

• "D1", "D2", ... "D9" (condensed identity coefficients)

Value

A positive number.

References

• Guo (1995) Proportion of genome shared identical by descent by relatives: concept, computation, and applications. Am J Hum Genet.

• Hill & Weir (2011). Variation in actual relationship as a consequence of Mendelian sampling and linkage. Genet Res.

• Thompson (2013). Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations. Genetics.

Examples

###################################
### Box 1 of Hill & Weir (2011) ###
###################################

# Eq. 4b of Hill & Weir
phi = function(n, l) {
 1/(2*l^2) * (1/4)^n * sum(sapply(1:n, function(r)
   choose(n, r) * (2*r*l - 1 + exp(-2*r*l))/r^2))
}

# Chromosome of 1 Morgan
L = 1

### Full sibs ###

## Not run: 
x = nuclearPed(2)
realisedIbdVariance(x, ids = 3:4, coeff = "k2", L = L)

# Hill & Weir (Box 1)
16*phi(4,L) - 16*phi(3,L) + 8*phi(2,L) - 2*phi(1,L)

## End(Not run)

### Double first cousins ###

## Not run: 
dfc = doubleFirstCousins()

# Runtime ~1 min
realisedIbdVariance(dfc, coeff = "k0", L = L)
realisedIbdVariance(dfc, coeff = "k1", L = L)
realisedIbdVariance(dfc, coeff = "k2", L = L)

# Hill & Weir, Box 1
var_k2 = 64*phi(8,L) - 64*phi(7,L) + 40*phi(6,L) - 20*phi(5,L) +
  33/4*phi(4,L) - 5/2*phi(3,L) + 5/8*phi(2,L)-1/8*phi(1,L)
var_k1 = 4*var_k2
var_k0 = var_k2 + 2 * (4*phi(4,L) - 2*phi(3,L) + 3/4*phi(2,L) - 1/4*phi(1,L))

var_k0
var_k1
var_k2

## End(Not run)

---

Add points to the IBD triangle

Description

Utility function for plotting kappa coefficients in the IBD triangle. This was previously only implemented as a base R plot, but is now also available in ggplot2 and plotly formats, controlled by the argument plotType. Labels are often easier to read in the two latter versions: The ggplot2 version uses ggrepel to separate labels, while plotly enables interactive exploration of the plot.

Usage

showInTriangle(
  kappa,
  plotType = c("base", "ggplot2", "plotly"),
  new = TRUE,
  ped = NULL,
  pedBL = c(0.5, 0.5),
  pedArgs = NULL,
  col = 6,
  cex = 1,
  pch = 4,
  lwd = 2,
  jitter = NULL,
  labels = NULL,
  colLab = col,
  cexLab = 0.8,
  labSep = "-",
  pos = 1,
  adj = NULL,
  keep.par = TRUE,
  ...
)

Arguments

kappa	Coordinates of points to be plotted in the IBD triangle. Valid input types are: A numerical vector of length 2 (kappa0, kappa2) or 3 (kappa0, kappa1, kappa2). In the latter case kappa1 is ignored. A matrix of data frame, whose column names must include either k0 and k2, kappa0 and kappa2, or ibd0 and ibd2. A list (and not a data frame), in which case an attempt is made to bind the elements row-wise.
plotType	Either "base" (default), "ggplot2" or "plotly". Abbreviations are allowed.
new	A logical indicating if a new triangle should be drawn.
ped	A pedigree to be drawn in the upper right corner of the plot. Default: NULL. This only works when plotType is base or ggplot2.
pedBL	A vector of length two, with entries in ⁠[0,1]⁠, indicating the coordinates of the bottom left corner. Default: c(0.5, 0.5).
pedArgs	Plotting arguments for the inset pedigree. Default: NULL.
col, cex, pch, lwd	Parameters controlling the appearance of points.
jitter	A logical. If NULL (default), jittering is disabled for plotType's "base" or "ggplot2" and enabled for "plotly".
labels	A character of same length as the number of points, or a single logical TRUE or FALSE. If TRUE, labels are created by pasting columns id1 and id2 in kappa (if these exist) separated by labSep. By default, labels are disabled when plotType = "base", enabled if plotType = "ggplot2" and enabled (interactively) if plotType = "plotly".
colLab, cexLab, pos, adj	Parameters controlling the appearance of labels. Ignored when plotType = "plotly".
labSep	A string, by default "-".
keep.par	A logical. If TRUE (and plotType = "base"), the graphical parameters are not reset after plotting, which may be useful for adding additional annotation.
...	Plot arguments passed on to ibdTriangle().

Value

If plotType = 'base', the function returns NULL; otherwise the plot object.

See Also

ibdTriangle(), kappaIBD()

Examples

showInTriangle(c(3/8, 1/8), label = "3/4 siblings", pos = 1)

# With inset pedigree
x = doubleCousins(1, 0, half2 = TRUE)
showInTriangle(c(3/8, 1/8), label = "3/4 siblings", pos = 1,
               ped = x, pedArgs = list(hatched = 6:7))

# All pairs
k = kappaIBD(x)
showInTriangle(k, labels = TRUE, pos = 1:4, ped = x)

# With jitter and variable colors
showInTriangle(k, labels = TRUE, pos = 1:4, jitter = TRUE, col = 1:7, ped = x)

# Separate labels (requires ggplot2 + ggrepel)
# showInTriangle(k, plot = "ggplot2", col = 2:8, ped = x)

# Interactive plot (requires plotly)
# showInTriangle(k, plot = "plotly", col = 2:8, pch = 0)

---

Two-locus IBD coefficients

Description

Computes the 3*3 matrix of two-locus IBD coefficients of a pair of non-inbred pedigree members, for a given recombination rate.

Usage

twoLocusIBD(
  x,
  ids,
  rho,
  coefs = NULL,
  detailed = FALSE,
  uniMethod = 1,
  verbose = FALSE
)

Arguments

x	A pedigree in the form of a pedtools::ped object.
ids	A character (or coercible to character) containing ID labels of two pedigree members.
rho	A number in the interval $[0, 0.5]$; the recombination rate between the two loci.
coefs	A character indicating which coefficient(s) to compute. A subset of c('k00', 'k01', 'k02', 'k10', 'k11', 'k12', 'k20', 'k21', 'k22'). By default, all coefficients are computed.
detailed	A logical, indicating whether the condensed (default) or detailed coefficients should be returned.
uniMethod	Either 1 or 2 (for testing purposes)
verbose	A logical.

Details

Let A, B be two pedigree members, and L1, L2 two loci with a given recombination rate $\rho$. The two-locus IBD coefficients $\kappa_{i,j}(\rho)$, for $0 \le i,j \le 2$ are defined as the probability that A and B have i alleles IBD at L1 and j alleles IBD at L2 simultaneously. Note that IBD alleles at the two loci are not required to be in cis (or in trans for that matter).

The method of computation depends on the (single-locus) IBD coefficient $\kappa_2$. If this is zero (e.g. if A is a direct ancestor of B, or vice versa) the two-locus IBD coefficients are easily computable from the two-locus kinship coefficients, as implemented in twoLocusKinship(). In the general case, the computation is more involved, requiring generalised two-locus kinship coefficients. This is implemented in the function twoLocusGeneralisedKinship(), which is not exported yet.

Value

By default, a symmetric 3*3 matrix containing the two-locus IBD coefficients $\kappa_{i,j}$.

If either coefs is explicitly given (i.e., not NULL), or detailed = TRUE, the computed coefficients are returned as a named vector.

See Also

twoLocusKinship(), twoLocusIdentity(), twoLocusPlot()

Examples

# Plot title used in several examples below
main = expression(paste("Two-locus IBD:  ", kappa[`1,1`]))

###################################################################
# Example 1: A classic example of three relationships with the same
# one-locus IBD coefficients, but different two-locus coefficients.
# As a consequence, these relationships cannot be separated using
# unlinked markers, but are (theoretically) separable with linked
# markers.
###################################################################
peds = list(
    GrandParent = list(ped = linearPed(2),   ids = c(1, 5)),
    HalfSib     = list(ped = halfSibPed(),   ids = c(4, 5)),
    Uncle       = list(ped = avuncularPed(), ids = c(3, 6)))

twoLocusPlot(peds, coeff = "k11", main = main, lty = 1:3, col = 1)


############################################################
# Example 2: Inspired by Fig. 3 in Thompson (1988),
# and its erratum: https://doi.org/10.1093/imammb/6.1.1.
#
# These relationships are also analysed in ?twoLocusKinship,
# where we show that they have identical two-locus kinship
# coefficients. Here we demonstrate that they have different
# two-locus IBD coefficients.
############################################################

peds = list(
  GreatGrand = list(ped = linearPed(3),              ids = c(1, 7)),
  HalfUncle  = list(ped = avuncularPed(half = TRUE), ids = c(4, 7))
)

twoLocusPlot(peds, coeff = "k11", main = main, lty = 1:2, col = 1)


########################################################################
# Example 3: Fig. 15 of Vigeland (2021).
# Two-locus IBD of two half sisters whose mother have inbreeding
# coefficient 1/4. We compare two different realisations of this:
#   PO: the mother is the child of parent-offspring
#  SIB: the mother is the child of full siblings
#
# The fact that these relationships have different two-locus coefficients
# exemplifies that a single-locus inbreeding coefficient cannot replace
# the genealogy in analyses of linked loci.
########################################################################

po = addChildren(nuclearPed(1, sex = 2), 1, 3, nch = 1, sex = 2)
po = addDaughter(addDaughter(po, 4), 4)

sib = addChildren(nuclearPed(2, sex = 1:2), 3, 4, nch = 1)
sib = addDaughter(addDaughter(sib, 5), 5)

# plotPedList(list(po, sib), new = TRUE, title = c("PO", "SIB"))

# List of pedigrees and ID pairs
peds = list(PO =  list(ped = po,  ids = leaves(po)),
            SIB = list(ped = sib, ids = leaves(sib)))

twoLocusPlot(peds, coeff = "k11", main = main, lty = 1:2, col = 1)


### Check against exact formulas
rho = seq(0, 0.5, length = 11)  # recombination values

kvals = sapply(peds, function(x)
  sapply(rho, function(r) twoLocusIBD(x$ped, x$ids, r, coefs = "k11")))

k11.po = 1/8*(-4*rho^5 + 12*rho^4 - 16*rho^3 + 16*rho^2 - 9*rho + 5)
stopifnot(all.equal(kvals[, "PO"], k11.po, check.names = FALSE))

k11.s = 1/16*(8*rho^6 - 32*rho^5 + 58*rho^4 - 58*rho^3 + 43*rho^2 - 20*rho + 10)
stopifnot(all.equal(kvals[, "SIB"], k11.s, check.names = FALSE))


################################################
# Example 4:
# The complete two-locus IBD matrix of full sibs
################################################

x = nuclearPed(2)
k2_mat = twoLocusIBD(x, ids = 3:4, rho = 0.25)
k2_mat

### Compare with exact formulas
IBDSibs = function(rho) {
  R = rho^2 + (1-rho)^2
  nms = c("ibd0", "ibd1", "ibd2")
  m = matrix(0, nrow = 3, ncol = 3, dimnames = list(nms, nms))
  m[1,1] = m[3,3] = 0.25 *R^2
  m[2,1] = m[1,2] = 0.5 * R * (1-R)
  m[3,1] = m[1,3] = 0.25 * (1-R)^2
  m[2,2] = 0.5 * (1 - 2 * R * (1-R))
  m[3,2] = m[2,3] = 0.5 * R * (1-R)
  m
}

stopifnot(all.equal(k2_mat, IBDSibs(0.25)))


#####################################################
# Example 5: Two-locus IBD of quad half first cousins
#
# We use this to exemplify two simple properties of
# the two-locus IBD matrix.
#####################################################

x = quadHalfFirstCousins()
ids = leaves(x)

# First compute the one-locus IBD coefficients (= c(17, 14, 1)/32)
k1 = kappaIBD(x, ids)

### Case 1: Complete linkage (`rho = 0`).
# In this case the two-locus IBD matrix has `k1` on the diagonal,
# and 0's everywhere else.
k2_mat_0 = twoLocusIBD(x, ids = ids, rho = 0)

stopifnot(all.equal(k2_mat_0, diag(k1), check.attributes = FALSE))

#' ### Case 2: Unlinked loci (`rho = 0.5`).
# In this case the two-locus IBD matrix is the outer product of
# `k1` with itself.
k2_mat_0.5 = twoLocusIBD(x, ids = ids, rho = 0.5)
stopifnot(all.equal(k2_mat_0.5, k1 %o% k1, check.attributes = FALSE))


########################################################
# Example 6: By Donnelly (1983) these relationships are
# genetically indistinguishable
########################################################

x1 = halfCousinPed(1)
x2 = halfCousinPed(0, removal = 2)
stopifnot(identical(
  twoLocusIBD(x1, ids = leaves(x1), rho = 0.25),
  twoLocusIBD(x2, ids = leaves(x2), rho = 0.25)))


###########################################################
# Example 7: Detailed coefficients of double first cousins.
# Compare with exact formulas by Denniston (1975).
###########################################################

## Not run: 
x = doubleFirstCousins()
ids = leaves(x)
rho = 0.25

kapDetailed = twoLocusIBD(x, ids, rho, detailed = TRUE)

# Example 1 of Denniston (1975)
denn = function(rho) {
  F = (1-rho)^2 * (rho^2 + (1-rho)^2)/4 + rho^2/8
  U = 1 + 2*F
  V = 1 - 4*F

  # Note that some of Denniston's definitions differ slightly;
  # some coefficients must be multiplied with 2
  c(k00 = U^2/4,
    k01 = U*V/8  *2,
    k02 = V^2/16,
    k10 = U*V/8  *2,
    k11.cc = F*U/2  *2,
    k11.ct = 0,
    k11.tc = 0,
    k11.tt = V^2/16  *2,
    k12.h = F*V/4  *2,
    k12.r = 0,
    k20 = V^2/16,
    k21.h = F*V/4  *2,
    k21.r = 0,
    k22.h = F^2,
    k22.r = 0)
}

stopifnot(all.equal(kapDetailed, denn(rho)))

## End(Not run)

---

Two-locus identity coefficients

Description

Computes the 9*9 matrix of two-locus condensed identity coefficients of a pair of pedigree members, for a given recombination rate.

Usage

twoLocusIdentity(x, ids, rho, coefs = NULL, detailed = FALSE, verbose = FALSE)

Arguments

x	A pedigree in the form of a pedtools::ped object.
ids	A character (or coercible to character) containing ID labels of two pedigree members.
rho	A number in the interval $[0, 0.5]$; the recombination rate between the two loci.
coefs	A character indicating which coefficient(s) to compute. A subset of c('D00', 'D01', ..., 'D99'). By default, all coefficients are computed.
detailed	A logical, indicating whether the condensed (default) or detailed coefficients should be returned.
verbose	A logical.

Details

Let A, B be two pedigree members, and L1, L2 two loci with a given recombination rate $\rho$. The two-locus identity coefficient $\Delta_{i,j}(\rho)$, for $1 \le i,j \le 9$ is defined as the probability that the identity state of the alleles of A and B are $\Sigma_i$ at L1 and $\Sigma_j$ at L2 simultaneously. (The ordering of the 9 states follows Jacquard (1974).)

For details about the algorithm, see Vigeland (2022).

Value

By default, a symmetric 9*9 matrix containing the two-locus condensed identity coefficients $\Delta_{i,j}$.

If either coefs is explicitly given (i.e., not NULL), or detailed = TRUE, the computed coefficients are returned as a named vector.

References

• Jacquard (1974). The Genetic Structure of Populations. Springer.

• Vigeland (2022) Two-locus identity coefficients in pedigrees (In progress)

See Also

twoLocusIBD(), identityCoefs()

Examples

### Full sibs ###
x = nuclearPed(2)
kapp = twoLocusIBD(x, ids = 3:4, rho = 0.25)
jacq = twoLocusIdentity(x, ids = 3:4, rho = 0.25)

stopifnot(all.equal(jacq[9:7,9:7], kapp, check.attributes = FALSE))

### Parent-child ###
x = nuclearPed(1)
jacq = twoLocusIdentity(x, ids = c(1,3), rho = 0.25)

stopifnot(jacq[8,8] == 1)

### Full sib mating ###
x = fullSibMating(1)
j = condensedIdentity(x, ids = 5:6)
j2 = twoLocusIdentity(x, ids = 5:6, rho = 0.25)

stopifnot(identical(unname(rowSums(j2)), j))

---

Two-locus inbreeding

Description

Computes the two-locus inbreeding coefficient of a pedigree member, for a given recombination rate.

Usage

twoLocusInbreeding(x, id, rho, verbose = FALSE, debug = FALSE)

Arguments

x	A pedigree in the form of a pedtools::ped object.
id	The ID label of a pedigree member.
rho	A numeric vector of recombination rates; all entries must be in the interval $[0, 0.5]$.
verbose	A logical.
debug	A logical. If TRUE, detailed messages are printed during the recursion process.

Details

Let A be a pedigree member, and L1, L2 two autosomal loci with recombination rate $\rho$. The two-locus inbreeding coefficient $f_{11}(\rho)$ is defined as the probability that A is autozygous at both L1 and L2 simultaneously.

As in the one-locus case, the two-locus inbreeding coefficient of A equals the two-locus kinship coefficient of the parents.

References

Weir & Cockerham (1969). Pedigree mating with two linked loci. Genetics, 61:923-940.

See Also

twoLocusKinship(), twoLocusIBD(), twoLocusIdentity()

Examples

###################################################
# Reproducing an example of Weir & Cockerham (1969)
###################################################

# Pedigree
x = nuclearPed(2, sex = 1:2) |>
  addDaughter(3:4) |>
  addSon(c(3,5)) |>
  addDaughter(5:6) |>
  relabel(new = strsplit("GHDECBA","")[[1]])

plot(x)

# The two-locus inbreeding of A
twoLocusPlot(list(ped = x, ids = "A"), coeff = "inb")

# W&C formula (expressed by linkage parameter a = 1-2*rho)
rho = seq(0, 0.5, length = 11)
a = 1 - 2*rho
WC = (128 + 10*a + 36*a^2 + 47*a^3 + 20*a^4 + 10*a^5 + 4*a^6 + a^7)/512

points(rho, WC, col = 2)

---

Two-locus kinship coefficients

Description

Computes the two-locus kinship coefficient of a pair of pedigree members, at a given recombination rate.

Usage

twoLocusKinship(
  x,
  ids,
  rho,
  recombinants = NULL,
  verbose = FALSE,
  debug = FALSE
)

Arguments

x	A pedigree in the form of a pedtools::ped object.
ids	A character (or coercible to character) containing ID labels of two or more pedigree members.
rho	A numeric vector of recombination rates; all entries must be in the interval $[0, 0.5]$.
recombinants	A logical of length 2, applicable only when ids has length 2. When given, it indicates whether each of the two gametes is a recombinant or non-recombinant. This parameter is mainly used by twoLocusIBD().
verbose	A logical.
debug	A logical. If TRUE, detailed messages are printed during the recursion process.

Details

Let A, B be two pedigree members, and L1, L2 two loci with a given recombination rate rho. The two-locus kinship coefficient $\phi_{AB}(rho)$ is defined as the probability that random gametes segregating from A and B has IBD alleles at both L1 and L2 simultaneously.

The implementation is based on the recursive algorithm described by Thompson (1988).

References

E. A. Thompson (1988). Two-locus and Three-locus Gene Identity by Descent in Pedigrees. IMA Journal of Mathematics Applied in Medicine & Biology, vol. 5.

Examples

######################
# Example 1: Full sibs
######################
x = nuclearPed(2)

k_0 = twoLocusKinship(x, ids = 3:4, rho = 0)
k_0.5 = twoLocusKinship(x, ids = 3:4, rho = 0.5)

stopifnot(k_0 == 1/4, k_0.5 == 1/16)


##################################################
# Example 2: Reproducing Fig. 3 in Thompson (1988)
# Note that in the article, curve (a) is wrong.
# See Erratum: https://doi.org/10.1093/imammb/6.1.1
##################################################

# Pedigrees (a) - (d)
ped.a = linearPed(3)
ped.b = avuncularPed(half = TRUE)
ped.c = cousinPed(1)
ped.d = doubleCousins(1, 1, half1 = TRUE, half2 = TRUE)

peds = list(
  a = list(ped = ped.a, ids = c(1,7)),
  b = list(ped = ped.b, ids = leaves(ped.b)),
  c = list(ped = ped.c, ids = leaves(ped.c)),
  d = list(ped = ped.d, ids = leaves(ped.d))
)

twoLocusPlot(peds, coeff = "kinship", lty = 1:4)

---

Two-locus coefficient plot

Description

Plot two-locus kinship or IBD coefficients as function of the recombination rate.

Usage

twoLocusPlot(
  peds,
  coeff = "k11",
  rseq = seq(0, 0.5, length = 11),
  xlab = "Recombination rate",
  ylab = NA,
  col = seq_along(peds),
  lty = 1,
  lwd = 1,
  ...
)

Arguments

peds	A list of lists. See details.
coeff	A string identifying which coefficient to compute. See Details for legal values.
rseq	A numeric vector of recombination rates. By default seq(from = 0, by = 0.5, length = 11).
xlab, ylab	Axis labels.
col, lty, lwd	Plotting parameters.
...	Further parameters passed on to matplot().

Details

Each entry of peds must be a list with the following (named) entries:

• ped: A ped object

• ids: A pair of labels identifying two members of ped

The coeff parameter must be either a character naming the coefficient to compute, or a function. If a character, it must be one of the following names: "inb", "kinship", "phi", "phi11", "k00", "k01", "k02", "k10", "k11", "k12", "k20", "k21" or "k22".

If coeff is a function, it must take three arguments named ped, ids and rho, and produce a single number for each set of input data. See Examples.

The first three are synonymous and indicate the two-locus kinship coefficient. The remaining choices are two-locus IBD coefficients. (See twoLocusIBD().)

Examples

###############################
# Classic example of three relationships with equal one-locus coeffs
peds = list(
    GrandParent = list(ped = linearPed(2),   ids = c(1, 5)),
    HalfSib     = list(ped = halfSibPed(),   ids = c(4, 5)),
    Uncle       = list(ped = avuncularPed(), ids = c(3, 6)))

twoLocusPlot(peds, coeff = "kinship")
twoLocusPlot(peds, coeff = "k11")

###############################

peds = list(
    PO = list(ped = nuclearPed(1), ids = c(1,3)),
    S  = list(ped = nuclearPed(2), ids = c(3,4)))

twoLocusPlot(peds, coeff = "kinship")
twoLocusPlot(peds, coeff = "k11")

###############################

ped1 = addChildren(halfSibPed(sex2 = 2), 4, 5, nch = 2)
ped2 = addChildren(linearPed(2, sex = 1:2), 1, 5, nch = 2)
ped3 = addChildren(avuncularPed("uncle", "niece"), 3, 6, nch = 2)

peds = list(
   `H-sibs` = list(ped = ped1, ids = leaves(ped1)),
   `G-sibs` = list(ped = ped2, ids = leaves(ped2)),
   `U-sibs` = list(ped = ped3, ids = leaves(ped3))
)
# plotPedList(peds)
twoLocusPlot(peds, coeff = "kinship")

################################

### Reproducing Fig 2 of Bishop & Williamson (1990)
### This example illustrates `coeff` as a function.

# The coefficient d11(rho) is the conditional probability of IBD = 1
# in the first locus, given IBD = 1 in the second.

G = linearPed(2)
H = halfSibPed()
U = avuncularPed()
FC = cousinPed(1)
FC1R = cousinPed(1, removal = 1)
SC = cousinPed(2)

peds = list(
    GrandParent = list(ped = G,    ids = c(1, 5)),
    HalfSib     = list(ped = H,    ids = leaves(H)),
    Uncle       = list(ped = U,    ids = leaves(U)),
    FirstCous   = list(ped = FC,   ids = leaves(FC)),
    FirstCous1R = list(ped = FC1R, ids = leaves(FC1R)),
    SecondCous  = list(ped = SC,   ids = leaves(SC)))


d11 = function(ped, ids, rho) {
  twoLocusIBD(ped, ids, rho, coefs = "k11")/kappaIBD(ped, ids)[2]
}

twoLocusPlot(peds, coeff = d11)

---