extractGenicFeatures: Generate a list of genic features GRangesList objects

In fagostini/Mimir: Metadata profiles for NGS data

Description

This function extracts and filters the genic features from a GenomicFeatures object.

Usage

extractGenicFeatures(TxDb = NULL, tx2gene = NULL, selectGn = NULL,
  selectTx = NULL, excludeIntrons = TRUE, bins = c(20, 100, 70, 100),
  verbose = TRUE)

Arguments

TxDb	A GenomicFeatures object. It must contain GenomeInfoDb information.
tx2gene	A "data.frame" object. The first column must be of transcript identifiers, while the second must be of gene identifiers. Additional columns will be discarded.
selectGn	A vector of optional gene identifiers to keep.
selectTx	A vector of optional transcript identifiers to keep.
excludeIntrons	When set to 'TRUE', the extraction of intronic regions is skipped.
bins	A 4 integers ordered vector. The vector order determines the 5'UTR, CDS, 3'UTR and Introns minumum region widths.
verbose	When set to 'TRUE', the function prints diagnostic messages.

Value

A named list of GenomicRanges objects.

Examples

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

genicRegions = extractGenicFeatures(TxDb = TxDb.Dmelanogaster.UCSC.dm3.ensGene)

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