Compute kinship matrix for IBD probabilities

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 chr for chromosome and pos for position. Positions should be in centimorgan (cM). They should not be cumulative over the chromosomes. Other columns are ignored. Marker names should be in the row names. These should match the marker names in the input file. Only required if chrSpecific = TRUE.
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)