plotGeneCoverage: Genomic plots with rnaSeqMap

In rnaSeqMap: rnaSeq secondary analyses

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

Author(s)

Michal Okoniewski, Anna Lesniewska

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
#  }

rnaSeqMap documentation built on Nov. 8, 2020, 5:50 p.m.