Description Usage Arguments Details Value Examples
Harvest contents of a TransStore by rank in associations of features to SNP.
1 | tsByRankAccum(tsin, maxrank = 3, mcol2keep=c("REF", "ALT", "snp", "MAF", "z.HWE"), filt=force)
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tsin |
An instance of |
maxrank |
The maximum rank of association scores to retrieve, cumulatively. Each variant has been tested for association with each genomic feature (e.g., gene in a typical expression QTL study), but only the top ranking associations are recorded for each variant. If maxrank=k, for each variant, this function retrieves the features exhibiting the kth largest association recorded over all features, along with all k-1 larger association scores. |
mcol2keep |
a character vector of metadata columns to retain |
filt |
a function accepting a GRanges and returning
a GRanges. The mcols of the GRanges to be processed
will have elements
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tsByRankAccum_sing and other functions with suffix _sing were developed for the case of a single permutation
getTransRegistries() accesses objects packaged for demonstration purposes
A GRanges
instance.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ## Not run: # dec 2017 -- BatchJobs registry must be updated
if (require(doParallel)) {
registerDoSEQ()
lit = TransStore(getTransRegistries()) # very limited slice
tbga = tsByRankAccum(lit, maxrank=5)
plot(ecdf(as.numeric(data.matrix(tbga$permscoresByRank1))), ylim=c(.99,1),
main="eCDF of permutation dist. of association, by variant rank")
exr = paste0("permscoresByRank", 2:5)
for (i in 1:4)
lines(ecdf(as.numeric(data.matrix(mcols(tbga)[[exr[i]]]))), col=i+1)
legend(200, .994, lty=1, col=1:5, legend=paste("rank", 1:5))
plot(ecdf(as.numeric(data.matrix(tbga$permscoresByRank1[,1]))), ylim=c(.99,1),
main="between-permutation variation")
lines(ecdf(as.numeric(data.matrix(tbga$permscoresByRank1[,2]))),col=2)
lines(ecdf(as.numeric(data.matrix(tbga$permscoresByRank1[,3]))),col=3)
lines(ecdf(as.numeric(data.matrix(tbga$permscoresByRank5[,1]))),col=4)
lines(ecdf(as.numeric(data.matrix(tbga$permscoresByRank5[,2]))),col=5)
lines(ecdf(as.numeric(data.matrix(tbga$permscoresByRank5[,3]))),col=6)
legend(200, .994, col=1:6, lty=1, legend=c("rank 1 (perm 1)", "(2)", "(3)",
"rank 5 (perm 1)", "(2)", "(3)"))
# head(tbga,2)
# consider the following filtering utility
# tbfilt = function(tbg, seqnames.="17", minMAF=.1, minabsodist = 1e7,
# nrec=1000) {
# tbg = tbg[ which(as.character(seqnames(tbg)) %in% seqnames.) ]
# tbg = tbg[ which(tbg$MAF > minMAF) ]
# tbg[ order(tbg$scores, decreasing=TRUE) ][1:nrec]
# }
}
## End(Not run)
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