Title: Inbreeding and Numerator Relationship Coefficients
Version: 1.1.0
Description: Compute inbreeding coefficients using the method of Meuwissen and Luo (1992) <doi:10.1186/1297-9686-24-4-305>, and numerator relationship coefficients between individuals using the method of Van Vleck (2007) https://pubmed.ncbi.nlm.nih.gov/18050089/.
License: GPL (≥ 3)
Encoding: UTF-8
RoxygenNote: 7.3.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/nilforooshan/FnR
BugReports: https://github.com/nilforooshan/FnR/issues
NeedsCompilation: no
Packaged: 2024-05-02 10:40:01 UTC; monil0
Author: Mohammad Ali Nilforooshan ORCID iD [aut, cre]
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Repository: CRAN
Date/Publication: 2024-05-05 23:30:02 UTC

Compute numerator relationship coefficients between two distinct groups of individuals

Description

Compute numerator relationship coefficients between two distinct groups of individuals

Usage

calcR(ped, set1, set2, type = "notdam-notsire", f = c(), d = c())

Arguments

ped

: A data frame with integer columns corresponding to ID, SIRE, and DAM. IDs should be sequential, starting from 1. Missing parents (SIRE and DAM) are denoted as 0.

set1

: A set of individual IDs.

set2

: A set of individual IDs, distinct from set1.

type

: "notdam-notsire" (default), "sire-sire", or "dam-dam" relationships

"notdam-notsire"

requires set1 and set2 individuals not to be members of ped$DAM and ped$SIRE, respectively.

"sire-sire"

requires set1 and set2 individuals to be members of ped$SIRE.

"dam-dam"

requires set1 and set2 individuals to be members of ped$DAM.

f

: (Optional) If available, the vector of inbreeding coefficients for the whole pedigree (without dummy progeny) or from the previous calculation of inbreeding coefficients with less number of animals in the pedigree.

d

: (Optional) If available, the vector of the diagonal elements of the diagonal matrix D in \mathbf A = \mathbf{TDT}' where A is the numerator relationship matrix, for the whole pedigree (without dummy progeny) or from the previous calculation of inbreeding coefficients with less number of animals in the pedigree.

Value

: Numerator relationship coefficients between set1 and set2 individuals in the form of a matrix (a partition of the numerator relationship matrix A).

Examples

# A sample pedigree data frame:
ped <- data.frame(
    ID = 1:12,
    SIRE = c(0, 0, 0, 2, 2, 0, 4, 6, 0, 6, 10, 10),
    DAM = c(0, 0, 0, 1, 1, 0, 3, 5, 7, 8, 9, 0)
)

# Example 1: Calculate relationship coefficients between two groups of animals,
# one's members not among dams, and the members of the other not among sires.
calcR(ped, set1 = c(12, 6), set2 = c(11, 8), type = "notdam-notsire")
# Since `"notdam-notsire"` is the default type, `type = "notdam-notsire"` might be omitted.

# Example 2: Calculate relationship coefficients between dam 7 and dams 8 and 9.
calcR(ped, set1 = 7, set2 = 8:9, type = "dam-dam")

# Example 3: Calculate relationship coefficients between sires 2 & 6 and sires 4 & 10.
calcR(ped, set1 = c(2, 6), set2 = c(4, 10), type = "sire-sire")

# Example 5: Repeat example 2 with inbreeding coefficients provided.
f <- rep(0, 12)
f[10] <- 0.25
f[11] <- 0.015625
calcR(ped, set1 = 7, set2 = 8:9, type = "dam-dam", f = f)

# Example 6: Repeat example 3 with inbreeding and d coefficients provided.
d <- c(1, 1, 1, 0.5, 0.5, 1, 0.5, 0.5, 0.75, 0.5, 0.4375, 0.6875)
calcR(ped, set1 = c(2, 6), set2 = c(4, 10), type = "sire-sire", f = f, d = d)

Calculate inbreeding coefficients from scratch or resume for new individuals in the pedigree

Description

Calculate inbreeding coefficients from scratch or resume for new individuals in the pedigree

Usage

resume_inbreed(ped, f = c(), d = c(), export_d = FALSE)

Arguments

ped

: A data frame with integer columns corresponding to ID, SIRE, and DAM. IDs should be sequential, starting from 1. Missing parents (SIRE and DAM) are denoted as 0.

f

: (Optional) If available, the vector of inbreeding coefficients from the previous calculation of inbreeding coefficients with less number of animals in the pedigree.

d

: (Optional) If available, the vector of the diagonal elements of the diagonal matrix D in \mathbf A = \mathbf{TDT}' from the previous calculation of inbreeding coefficients with less number of animals in the pedigree, where A is the numerator relationship matrix.

export_d

: FALSE (default) or TRUE. If TRUE, vector d is retuned for future use.

Value

: Vector of inbreeding coefficients if export_d == FALSE, or a list containing the vector of inbreeding coefficients and the vector of d coefficients if export_d == TRUE.

Examples

# A sample pedigree data frame:
ped <- data.frame(
    ID = 1:12,
    SIRE = c(0, 0, 0, 2, 2, 0, 4, 6, 0, 6, 10, 10),
    DAM = c(0, 0, 0, 1, 1, 0, 3, 5, 7, 8, 9, 0)
)

oldped <- ped[1:9, ]
(oldrun <- resume_inbreed(oldped, export_d = TRUE))
resume_inbreed(ped)
resume_inbreed(ped, f = oldrun$f)
resume_inbreed(ped, f = oldrun$f, d = oldrun$d)