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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:

Packaged:

2024-05-02 10:40:01 UTC; monil0

Author:

Mohammad Ali Nilforooshan

[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 fromset1.

type

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

"notdam-notsire": requiresset1 andset2 individuals not to be members ofped$DAM andped$SIRE, respectively.
"sire-sire": requiresset1 andset2 individuals to be members ofped$SIRE.
"dam-dam": requiresset1 andset2 individuals to be members ofped$DAM.

f

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

Value

: Numerator relationship coefficients betweenset1 andset2 individuals in the form of a matrix (a partition of the numerator relationship matrixA).

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] <- 0.25f[11] <- 0.015625calcR(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 matrixD in\mathbf A = \mathbf{TDT}'from the previous calculation of inbreeding coefficients with less number of animals in the pedigree,whereA is the numerator relationship matrix.

export_d

:FALSE (default) orTRUE. IfTRUE, vectord is retuned for future use.

Value

: Vector of inbreeding coefficients ifexport_d == FALSE,or a list containing the vector of inbreeding coefficients and the vector ofd coefficients ifexport_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)