generateMergeTable: Generate Merge Table

In mfansler/txcutr: Transcriptome CUTteR

Description

Generate Merge Table

Usage

generateMergeTable(txdb, minDistance = 200)

## S4 method for signature 'TxDb'
generateMergeTable(txdb, minDistance = 200L)

Arguments

txdb	an object representing a transcriptome
minDistance	the minimum separation to regard overlapping transcripts as unique

Value

a data.frame with three columns - tx_in the input transcript - tx_out the transcript merged into - gene_out the gene merged into

a data.frame with three columns - tx_in the input transcript - tx_out the transcript merged into - gene_out the gene merged into

Examples

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

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

## restrict to 'chrI' transcripts
seqlevels(txdb) <- c("chrI")

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

## last 100 nts per tx
txdb_w100 <- truncateTxome(txdb, maxTxLength=100)
txdb_w100

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