A note on fimo16 in TFutils


Sequence-based TF affinity scoring can be conducted with the FIMO suite, see @Sonawane2017. We have serialized an object with references to FIMO outputs for 16 TFs.


While the token bed is used in the filenames, the files are not actually bed format!

Importing with scanTabix

We can use reduceByRange to import selected scans.

si = TFutils::seqinfo_hg19_chr17
myg = GRanges("chr17", IRanges(38.07e6,38.09e6), seqinfo=si)
colnames(fimo16) = fimo16$HGNC 
lk2 = reduceByRange(fimo16[, c("POU2F1", "VDR")],
  MAP=function(r,f) scanTabix(f, param=r))

This result can be massaged into a GRanges or other desirable structure. fimo_granges takes care of this.

#fimo_ranges = function(gf, query) { # prototypical code
# rowRanges(gf) = query
# ans = reduceByRange(gf, MAP=function(r,f) scanTabix(f, param=r))
# ans = unlist(ans, recursive=FALSE)  # drop top list structure
# tabs = lapply(ans, lapply, function(x) {
#     con = textConnection(x)
#     on.exit(close(con))
#     dtf = read.delim(con, h=FALSE, stringsAsFactors=FALSE, sep="\t")
#     colnames(dtf) = c("chr", "start", "end", "rname", "score", "dir", "pval")
#     ans = with(dtf, GRanges(seqnames=chr, IRanges(start, end),
#            rname=rname, score=score, dir=dir, pval=pval))
#     ans
#     })
# GRangesList(unlist(tabs, recursive=FALSE))
rr = fimo_granges(fimo16[, c("POU2F1", "VDR")], myg)

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TFutils documentation built on May 2, 2020, 2:01 a.m.