fimo_granges {TFutils} | R Documentation |
create a list of GRanges for FIMO hits in a GenomicFiles instance, corresponding to a GRanges-based query
fimo_granges(gf, query)
gf |
GenomicFiles instance, like fimo16 in TFutils |
query |
a GRanges specifying ranges to check for TF binding scores |
a list of GRanges, produced by GenomicFiles::reduceByRange
Be sure to use register([BPPARAM])
appropriately.
if (interactive()) { # need internet # setup -- annotate fimo16 object and create an informative # query colnames(fimo16) = fimo16$HGNC si = GenomeInfoDb::Seqinfo(genome="hg19")["chr17"] # to fix query genome myg = GRanges("chr17", IRanges(38.07e6,38.09e6), seqinfo=si) requireNamespace("BiocParallel") BiocParallel::register(BiocParallel::SerialParam()) f1 = fimo_granges(fimo16[, c("VDR", "POU2F1")], myg) f1 }