fimo_granges {TFutils} | R Documentation

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

### Description

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

### Usage

    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

    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
    }

[Package TFutils version 1.14.0 Index]