splitGenesAcrossChroms: Split genes that have isoforms across chromosomes

Description Usage Arguments Value Examples

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

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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

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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)


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