transeqByCluster {GGtools} | R Documentation |
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
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, ...)
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 |
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 |
the TransConfig-class
instance determines
most of the details of the testing procedure
a data.frame with test results as chisq, and permScore* with scores obtained after permuting expression against genotype