transeqByCluster {GGtools} | R Documentation

## 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

### 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

[Package GGtools version 5.16.0 Index]