mergeTranscripts: mergeTranscripts

In karyoploteR: Plot customizable linear genomes displaying arbitrary data

Description

Merges the transcripts of each gene and creates one transcript per gene with all exons and UTR regions combined

Usage

mergeTranscripts(genes.data)

Arguments

genes.data

(GenesData object) A valid genes.dat object like the ones obtained by makeGenesDataFromTxDb

Details

This function takes a valid data object and merges all transcripts from each gene into a single transcript. This is useful to reduce the plot complexity while keeping partial information on transcript structure.#' In this transcript, any region that is a coding exon in any transcript, will be an exon, any region that is a non-coding exon in any transcript and is not an exon in any transcript, will be a non-coding exon. Anything between coding and non-coding exons will be introns.

Value

The original GenesData object with a single transcript per gene GenesData$genes$names.

See Also

kpPlotGenes, makeGenesDataFromTxDb

Examples

 
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

zoom <- toGRanges("chr17:29.4e6-29.8e6")
kp <- plotKaryotype(genome="hg19", zoom=zoom)
genes.data <- makeGenesDataFromTxDb(TxDb.Hsapiens.UCSC.hg19.knownGene, karyoplot=kp)
genes.data <- addGeneNames(genes.data)
kpPlotGenes(kp, data=genes.data, r1=0.5, plot.transcripts=TRUE, gene.name.position = "left")
genes.data.merged <- mergeTranscripts(genes.data)
kpPlotGenes(kp, data=genes.data.merged, r0=0.6, r1=0.8, plot.transcripts=TRUE, gene.name.position = "left")
 

karyoploteR documentation built on Nov. 8, 2020, 5:52 p.m.