Usage
pairscan.kin(data.obj, geno.obj = NULL, covar,
scan.what, marker.pairs, kin.full.geno,
sample.kinship, num.kin.samples, n.per.sample,
verbose = TRUE, n.cores = 2)
Arguments
geno.obj
The object in which the genotype matrix and marker information are stored. See read.geno.
covar
A vector of character strings indicating which covariates to use.
scan.what
A character string uniquely identifying whether eigentraits or raw traits should be scanned.
marker.pairs
A two-column matrix indicating which marker pairs to test in the pairscan.
kin.full.geno
A logical value indicating whether a kinship matrix for the entire genome should be calculated. This is TRUE if phenotypic covariates are being tested.
sample.kinship
A logical value indicating whether kinship matrices should be sampled (TRUE) or calculated directly (FALSE). Sampling is faster when very large genotype matrices are being used.
num.kin.samples
An integer indicating how many samples to use in calculating the kinship matrices if sample.kinship is TRUE.
n.per.sample
An integer indicating how many markers should be sampled in calculating the kinship matrices if sample.kinship is TRUE.
verbose
A logical value indicating whether the progress of the scan should be printed to the screen.
n.cores
An integer specifying the number of cores to be used in parallel processing.