gQTLstats (version 1.4.2)

transAssoc: 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

# 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))