txdbToGRangesList {txcutr}

R Documentation

Convert TxDb object to GRangesList

Description

Convert TxDb object to GRangesList

Usage

txdbToGRangesList(
  txdb,
  geneCols = c("gene_id"),
  transcriptCols = c("gene_id", "tx_name"),
  exonCols = c("gene_id", "tx_name", "exon_id", "exon_rank")
)

Arguments

txdb	a TxDb object
geneCols	names of columns to include in the genes ranges
transcriptCols	names of columns to include in the transcripts ranges
exonCols	names of columns to include in the exons ranges

Value

a GRangesList object with entries c(genes, transcripts, exons)

Examples

library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)

## load annotation
txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene

grl <- txdbToGRangesList(txdb)
grl

---