exportMergeTable: Export Merge Table for Transcriptome

In mfansler/txcutr: Transcriptome CUTteR

Description

Export Merge Table for Transcriptome

Usage

exportMergeTable(txdb, file, minDistance = 200L)

Arguments

txdb	a TxDb object representing a transcriptome annotation
file	a string or connection to output TSV file. Automatically recognizes strings ending with ".gz" for zipped output.
minDistance	the minimum separation to regard overlapping transcripts as unique.

Value

The txdb argument is invisibly returned.

Examples

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

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

## restrict to 'chrI' transcripts (makes for briefer example runtime)
seqlevels(txdb) <- c("chrI")

## last 500 nts per tx
txdb_w500 <- truncateTxome(txdb)

## export plain format
outfile <- tempfile("sacCer3.sgdGene.w500", fileext=".tsv")
exportMergeTable(txdb_w500, outfile)

## export compressed format
outfile <- tempfile("sacCer3.sgdGene.w500", fileext=".tsv.gz")
exportMergeTable(txdb_w500, outfile)

mfansler/txcutr documentation built on Dec. 21, 2021, 4:59 p.m.