plotGenesInChroms: ploGenesInChromosomes: A function to plot specific genes onto...

In bertamiro/lpattern: Detection of scatterplots with L-shaped pattern

Description

ploGenesInChromosomes Given a list of genes with their transcript coordenates, the function will plot the genes on their specific locations on each corresponding chromosme. It can also collocate the genes with CpG islands information and and DNAseI hypersesitive sites.

Usage

plotGenesInChroms(transcriptCoords, plotsFilename, minbase, maxbase,
  islandData, dnaseData)

Arguments

transcriptCoords	object of class containing a list of genes annotated with the getGenesLocations
plotsFilename	object with the name of the file that will be used to save the .pdf with the graphs.
minbase	number for the smallest basepair position of the chromosome. First position on the chromosome from the 5' side.
maxbase	number for the largest basepair position of the chromosome. Last position on the chomosome from the 5' side.
islandData	object of class GRanges containing CpG islands position data.
dnaseData	object of class GRanges containing DNAseI hypersensitive sites position data.

Details

The data for the cpG islands was obtained from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cpgIslandExt.txt.gz and the data for the DNAseI hypersensitive sites from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeRegDnaseClustered/ For both datasets, positions were annotated with GenomicRanges::GRanges().

Examples

## Not run: 
transcriptCoords <- getGenesLocations(rownames(selectedGenes),
csvFileName="results/coordsselectedGenes.csv")
starts <- min(lapply(transcriptCoords, function(tc){as.numeric(min(tc$TXSTART))}))
ends <- max(lapply(transcriptCoords, function(tc){as.numeric(max(tc$TXEND))}))

minbase <- starts - (0.25*(ends-starts)) #allow 25% extra space on the plot
maxbase <- ends + (0.25*(ends-starts))
islandHMM = read.csv(paste("dades", "model-based-cpg-islands-hg19.txt",sep="/"),
stringsAsFactors=FALSE, header=TRUE)
islandData <- GRanges(seqnames=Rle(islandHMM$chr),
                   ranges=IRanges(start=islandHMM$start, end=islandHMM$end),
                   strand=Rle(strand(rep("*",nrow(islandHMM)))))

dnase <- read.csv(paste("dades","wgEncodeRegDnaseClusteredV3.bed",sep="/"),
stringsAsFactors=FALSE,header=FALSE)
dnaseData <- GRanges(seqnames=dnase[,1],
                  ranges=IRanges(start=dnase[,2], end=dnase[,3]),
                  strand=Rle(rep("*",nrow(dnase))),
                  data=dnase[,5])

plotGenesInChromosomes(transcCoords, fileName, minbase, maxbase, islanData, dnaseData)

## End(Not run)

bertamiro/lpattern documentation built on July 19, 2019, 12:56 p.m.