transeqByCluster: convenience functions for trans-eQTL testing

In GGtools: software and data for analyses in genetics of gene expression

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

Details

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

Value

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

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.