rnaSeqMap (version 2.30.0)

plotGeneCoverage: Genomic plots with rnaSeqMap

Description

Various plots of genomic coverage for experiments.

Usage

plotGeneCoverage(gene_id, ex)
plotRegionCoverage(chr, start, end, strand, ex) 
plotExonCoverage (exon_id,ex)
plotCoverageHistogram (chr,start,end,strand,ex, skip)
plotGeneExonCoverage(gene_id, ex)
plotSI(chr,start,end,strand, exp1, exp2 )

Arguments

ex

vectors of experiment numbers to plot

exp1, exp2

experiment numbers for splicing index

gene_id

Ensembl gene ID

exon_id

Ensembl exon ID

chr

Chromosome

start

Start position of region on the chromosome

end

Start position of region on the chromosome

strand

Strand

skip

size of the bucket in histogram

Examples

#  if (xmapConnected())  
#  {
#    plotGeneCoverage( "ENSG00000144567", 1:3) # plotting FAM134A for experiments 1,2,3
#    plotRegionCoverage( 2, 220040947, 220050201, 1, 1:3 ) # the same, using coordinates
#  }