Count from beds to make count matrix

Count from beds to make count matrix

countFromBed(Bed, GR, notStranded = TRUE, interFeature = FALSE)

Arguments

Bed

BED bed files containing mapped reads.

GR

genomic ranges object over which to count.

notStranded

if strand information should be considered when counting, TRUE (ignore strand) or FALSE (consider strand; default).

interFeature

discard reads mapping to multiple features, TRUE or FALSE (default).

Value

count matrix.

Author

Kathryn Rozen-Gagnon

Examples

testFasta <- system.file("extdata/hg19Small.fa",package="CLIPflexR")
myIndex <-suppressWarnings(bowtie2_index(testFasta, overwrite = TRUE))