fimo_granges: create a list of GRanges for FIMO hits in a GenomicFiles...

Description Usage Arguments Value Note Examples

Description

create a list of GRanges for FIMO hits in a GenomicFiles instance, corresponding to a GRanges-based query

Usage

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fimo_granges(gf, query)

Arguments

gf

GenomicFiles instance, like fimo16 in TFutils

query

a GRanges specifying ranges to check for TF binding scores

Value

a list of GRanges, produced by GenomicFiles::reduceByRange

Note

Be sure to use register([BPPARAM]) appropriately.

Examples

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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
}

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