| Title: | Inbreeding and Numerator Relationship Coefficients |
|---|---|
| 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/>. |
| Authors: | Mohammad Ali Nilforooshan [aut, cre]
|
| Maintainer: | Mohammad Ali Nilforooshan <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 1.1.0 |
| Built: | 2025-02-13 03:11:21 UTC |
| Source: | https://github.com/nilforooshan/fnr |
Compute numerator relationship coefficients between two distinct groups of individuals
calcR(ped, set1, set2, type = "notdam-notsire", f = c(), d = c())calcR(ped, set1, set2, type = "notdam-notsire", f = c(), d = c())
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 |
type |
:
|
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 |
: Numerator relationship coefficients between set1 and set2 individuals in the form of a matrix (a partition of the numerator relationship matrix A).
# 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)# 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
resume_inbreed(ped, f = c(), d = c(), export_d = FALSE)resume_inbreed(ped, f = c(), d = c(), export_d = FALSE)
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 |
export_d |
: |
: 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.
# 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$d)# A sample pedigree data frame: ped <- data.frame( ID = 1:12, SIRE = c(0, 0, 0, 2, 2, 0, 4, 6, 0, 6, 10, 10), DAM = c(0, 0, 0, 1, 1, 0, 3, 5, 7, 8, 9, 0) ) oldped <- ped[1:9, ] (oldrun <- resume_inbreed(oldped, export_d = TRUE)) resume_inbreed(ped) resume_inbreed(ped, f = oldrun$f) resume_inbreed(ped, f = oldrun$f, d = oldrun$d)