transAssoc {gQTLstats} | R Documentation

## compute 'trans' SNP-feature associations by wrapping AllAssoc

### Description

compute 'trans' SNP-feature associations by wrapping AllAssoc, retaining only the strongest associations (and similarly filtered association scores computed under permutation)

### Usage

    transAssoc(variantGR, exSE, vcfgen, bufsize = 10, nperm = 3, exChLen = 2 * bufsize, ...)

### Arguments

`variantGR` | GRanges instance establishing scope of variants to test
`exSE` | SummarizedExperiment instance, all of whose features will be tested for association with all SNP
`vcfgen` | a function returning a path to a tabix-indexed VCF file from which SNP genotypes will be extracted
`bufsize` | Size of 'buffer' used to retain largest feature association scores encountered during the search. The scores and the names of associated genes are retained in 'scorebuf' and 'elnames' components of output GRanges
`nperm` | number of permutations of features against genotypes to be performed for realizing null distribution of association scores
`exChLen` | size of chunks of exSE to be tested through calls to AllAssoc; this is intended to allow control of RAM usage
`...` | arguments passed to AllAssoc

### Value

a GRanges with mcols including

### Examples

    ## Not run:   # requires acccess to 1KG S3
    library(geuvPack)
    data(geuFPKM)
    seqlevelsStyle(geuFPKM) = "NCBI"
    mysr = GRanges("20", IRanges(33000055, 33020055))
    genome(mysr) = "hg19"
    tt = transAssoc(mysr, geuFPKM[1:16,],
        bufsize=3, exChLen=4, vcfgen=function(x)gtpath(paste0("chr", x)) )
    colnames(mcols(tt))
    table(as.character(mcols(tt)$elnames))

    ## End(Not run)

[Package gQTLstats version 1.12.0 Index]