bindmaf {GGtools} | R Documentation |
bind testing metadata to a best.cis.eQTLs result
meta.bindmaf (smpackvec=c("GGdata", "hmyriB36"), smchr="20", obj, usemaxMAF=FALSE, SSgen=GGBase::getSS)
smpackvec |
a vector of candidate package names (potential
smpack arguments to |
smchr |
the chromosome name as used in the names of the |
obj |
an instance of |
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 |
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. |
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
a GRanges instance
This will be used to stratify the permuted scores.
## Not run: b1 = best.cis.eQTLs(chr="20") # sharply filtered b1b = bindmaf(obj=b1) ## End(Not run)