kinshipIBD {statgenMPP} | R Documentation |
Compute kinship matrix for IBD probabilities
Description
Compute a kinship matrix or a list of chromosome specific kinship matrices
for a 3D array of IBD probabilities. The kinship matrix is computed by
averaging Z Z^t
over all markers, where Z
is the genotype x
parents matrix for the marker. If chrSpecific = TRUE
chromosome
specific kinship matrices are computed for each chromosome based only on the
markers on all other chromosomes.
Usage
kinshipIBD(markers, map = NULL, chrSpecific = TRUE)
Arguments
markers |
An n x m x p array with IBD probabilities with genotypes in the rows (n), markers in the columns (m), and parents in the 3rd dimension (p). |
map |
A data.frame with columns |
chrSpecific |
Should chromosome specific kinship matrices be computed? |
Value
A kinship matrix or a list of chromosome specific kinship matrices.
Examples
## Read phenotypic data.
pheno <- read.delim(system.file("extdata/multipop", "AxBxCpheno.txt",
package = "statgenMPP"))
## Rename first column to genotype.
colnames(pheno)[1] <- "genotype"
## Compute IBD probabilities for simulated population - AxB, AxC.
ABC <- calcIBDMPP(crossNames = c("AxB", "AxC"),
markerFiles = c(system.file("extdata/multipop", "AxB.txt",
package = "statgenMPP"),
system.file("extdata/multipop", "AxC.txt",
package = "statgenMPP")),
pheno = pheno,
popType = "F4DH",
mapFile = system.file("extdata/multipop", "mapfile.txt",
package = "statgenMPP"),
evalDist = 5)
## Compute chromosome specific kinship matrices.
KChrSpec <- kinshipIBD(markers = ABC$markers, map = ABC$map)