GGtools (version 5.8.0)

transeqByCluster: convenience functions for trans-eQTL testing

Description

convenience functions for trans-eQTL testing, one assuming a parallel-based cluster instance is available, one assuming a chromosome's SNPs will all be candidates for testing

Usage

transeqByCluster(cl,  snpchrs = c("chr21", "chr22"),  exchrs = 1:22, baseconf,  targname = "transrun_", nperm = 1, inseed = 1234, ...)
transeqByChrom(snpchr = "chr22",  exchrs = 1:22, baseconf, targname = "transrun_",  nperm = 1, inseed = 1234, ...)

Arguments

cl

cluster instance as defined by the parallel package makeCluster API

snpchrs

character vector of tokens to be used to enumerate chromosomes harboring SNP for testing

snpchr

character atom, for transeqByChrom, the chromosome on which testing will be conducted

exchrs

enumeration of chromosomes harboring expression measures to be checked for trans association with SNPs

baseconf

an instance of TransConfig-class

targname

folder where scratch results are computed

nperm

number of permutations to be used for plug-in FDR

inseed

seed to be set before permutations are attempted, in conjunction with RNGkind("L'Ecuyer-CMRG")

...

not used

Value

a data.frame with test results as chisq, and permScore* with scores obtained after permuting expression against genotype

Details

the TransConfig-class instance determines most of the details of the testing procedure