extractGenomicFeatures: Generate a list of genomic features GRangesList objects

In fagostini/Mimir: Metadata profiles for NGS data

Description

This function extracts and filters gene, upstream and downstream features from a GenomicFeatures object.

Usage

extractGenomicFeatures(TxDb = NULL, selectGn = NULL,
  excludeIntrons = TRUE, exon_width = 1000, intron_width = 1000,
  upstream_width = 1000, downstream_width = 1000, verbose = TRUE)

Arguments

TxDb	A GenomicFeatures object. It must contain GenomeInfoDb information.
selectGn	A vector of optional gene identifiers to keep.
excludeIntrons	When set to 'TRUE', the extraction of intronic regions is skipped.
exon_width	A positive integer. It determines the minumum width for the sum of all exons in a gene.
intron_width	A positive integer. It determines the minumum width for the sum of all introns in a gene.
upstream_width	A positive integer. It determines the width of the upstream regions.
downstream_width	A positive integer. It determines the width of the downstream regions.
verbose	When set to 'TRUE', the function prints diagnostic messages.

Value

A named list of GenomicRanges objects.

Examples

library("TxDb.Dmelanogaster.UCSC.dm3.ensGene")

genomicRegions = extractGenomicFeatures(TxDb = TxDb.Dmelanogaster.UCSC.dm3.ensGene)

fagostini/Mimir documentation built on Dec. 3, 2019, 7:53 p.m.