mergeTranscripts | R Documentation |
Merges the transcripts of each gene and creates one transcript per gene with all exons and UTR regions combined
mergeTranscripts(genes.data)
genes.data |
(GenesData object) A valid genes.dat object like the ones obtained by |
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.
The original GenesData object with a single transcript per gene
GenesData$genes$names
.
kpPlotGenes
, makeGenesDataFromTxDb
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")
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