bed_file_filter: Extract a list of ranges defined by the bed_file_content_gr...

In metagene: A package to produce metagene plots

Description

Extract a list of ranges defined by the bed_file_content_gr argument from the ebgwot GRangesList. Equivalent to the exonsByOverlaps of GenomicFeatures.

Usage

bed_file_filter(ebgwot, bed_file_content_gr, reduce = TRUE)

Arguments

ebgwot	A GRangesList object provided by the exon_by_gene_with_observed_transcripts function.
bed_file_content_gr	A GRanges object containing ranges of interest.
reduce	If the returned GRanges object will be reduce or not.

Value

A GRanges object that contains exons by genes selected.

Examples

## Not run: 
   require(EnsDb.Hsapiens.v86)
   edb <- EnsDb.Hsapiens.v86
   quantification_files <- 'file_path'
   ebgwot <- exon_by_gene_with_observed_transcripts(edb, 
                                                   quantification_files)
   bed_file_content_gr <- GRanges("chr16",ranges = IRanges(start=23581002, 
                                                           end=23596356))
   bed_file_filter(ebgwot, bed_file_content_gr)

## End(Not run)

metagene documentation built on Nov. 8, 2020, 5:37 p.m.