bindmaf: bind testing metadata to a best.cis.eQTLs result

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

Description

bind testing metadata to a best.cis.eQTLs result

Usage

meta.bindmaf (smpackvec=c("GGdata", "hmyriB36"),
     smchr="20", obj, usemaxMAF=FALSE, SSgen=GGBase::getSS) 

Arguments

smpackvec	a vector of candidate package names (potential smpack arguments to getSS for metaanalysis across populations or tissues
smchr	the chromosome name as used in the names of the smList output for the getSS result
obj	an instance of mcwBestCis-class generated using the package named in smpack
usemaxMAF	if TRUE, label a SNP with maximum MAF observed across populations, otherwise compute the MAF for the combined genotypes across populations represented by the various smlSet instances generated with the smpackvec spec.
SSgen	function to be used to create smlSet instance for testing – in general, GGBase::getSS has been used to pull the ExpressionSet and SnpMatrix data from a named package, but in some cases a specialize task is needed to create the desired smlSet. Whatever is passed to SSgen must return an smlSet instance.

Details

computes the MAF of most highly associated SNP per gene, and distance between that SNP and the transcription limits of the gene, assigning 0 for this if the SNP lies within the transcription limits

Value

a GRanges instance

Note

This will be used to stratify the permuted scores.

Examples

## Not run: 
 b1 = best.cis.eQTLs(chr="20")  # sharply filtered
 b1b = bindmaf(obj=b1)
 
## End(Not run)

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