mergeTranscripts: mergeTranscripts

Description Usage Arguments Details Value See Also Examples

View source: R/genes.R

Description

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

Usage

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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

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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.