Usage
pairscan(data.obj, geno.obj = NULL, covar = NULL,
scan.what = c("eigentraits", "raw.traits"), total.perm = NULL,
min.per.genotype = NULL, max.pair.cor = NULL,
n.top.markers = NULL, use.kinship = FALSE, kin.full.geno = TRUE,
sample.kinship = TRUE, num.kin.samples = 100, n.per.sample = 100,
verbose = FALSE, num.pairs.limit = 1e6, num.perm.limit = 1e7,
overwrite.alert = TRUE, n.cores = NULL)
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 should be used in the regressions.
scan.what
A character string uniquely identifying whether eigentraits or raw traits should be scanned.
total.perm
The total number of permutations to be performed.
min.per.genotype
The minimum number of individuals allowable per genotype. If for a given marker pair, one of the genotypes is underrepresented, the marker pair is not tested. If this value is NULL, max.pair.cor must have a numeric value.
max.pair.cor
A numeric value between 0 and 1 indicating the maximum Pearson correlation that two markers are allowed. If the correlation between a pair of markers exceeds this threshold, the pair is not tested. If this value is set to NULL, min.per.genotype must have a numeric value.
n.top.markers
This optional integer is used in the generation of a null distribution. To generate the null, a singlescan is performed on permuted data and the top ranking markers are used in a pairscan. n.top.markers specifies how many of these markers should be chosen. If NULL, n.top.markers is the number of markers being scanned in the pairscan.
use.kinship
A logical value indicating whether a kinship correction should be implemented.
kin.full.geno
A logical value indicating whether the entire genotype matrix should be used to calculate kinship corrections. If FALSE, only the subset of genetic markers being scanned will be used to calculate kinship corrections.
sample.kinship
A logical value indicating whether kinship matrices should be sampled (TRUE) or calculated directly (FALSE). Sampling kinshp matrices can be faster in the case of very large genotype matrices.
num.kin.samples
If sample.kinship is TRUE, this integer indicates how many samples should be used to calculate kinship matrices.
n.per.sample
If sample.kinship is TRUE, this integer indicates how many markers should be used in each sample of the genotype matrix for calculating kinship matrices.
verbose
A logical value indicating whether the progress of the scan should be printed to the screen.
num.pairs.limit
A number indicating the maximum number of pairs to scan. If the number of pairs exceeds this threshold, the function asks for confirmation before proceeding with the pairwise scan.
num.perm.limit
A number indicating the maximum number of total permutations that will be performed. If the number of total permutations exceeds this threshold, the function asks for confirmation before proceeding with the pairwise scan.
overwrite.alert
If TRUE, this triggers an alert warning the user that the output of this function should be saved separately from the data.obj.
n.cores
An integer specifying the number of cores to be used in parallel processing. If NULL, the choice is made automatically.