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


[Package txcutr version 1.0.0 Index]