alpine (version 0.99.1)

splitGenesAcrossChroms: Split genes that have isoforms across chromosomes

Description

This function simply splits apart genes which have isoforms across multiple chromosomes. New "genes" are created with the suffix "_cs" and a number.

Usage

splitGenesAcrossChroms(ebg, txdf)

Arguments

ebg

an exons-by-genes GRangesList, created with exonsBy

txdf

a data.frame created by running select on a TxDb object. Must have columns TXCHROM and GENEID

Value

a list of manipulated ebg and txdf

Examples

library(GenomicRanges)
txdf <- data.frame(TXCHROM=c("1","1","2"),
                   GENEID=c("101","102","102")) 
ebg <- GRangesList(GRanges("1",IRanges(c(100,200),width=50)),
                   GRanges(c("1","2"),IRanges(c(400,100),width=50)))
names(ebg) <- c("101","102")
splitGenesAcrossChroms(ebg, txdf)