compEpiTools (version 1.6.3)

plotStallingIndex: Stalling Index plots

Description

generates the plot from the output of the stallingIndex function. The plot has 3 panels: Stalling Index, TSS and gene body

Usage

plotStallingIndex(matlist, xlimlist=NULL,
colors=rainbow(length(matlist)))

Arguments

matlist

List of matrices; each matrix must have a TSS, GB and SI column, as in the output of the function stallingIndex

xlimlist

List of numeric vectors (optional); ranges for the x axis of the three plots. The list must have 3 elements named 'SI', 'TSS' and 'GB'. Default:NULL

colors

array; names of the colors used for the lines in the plot. Default:rainbow palette

Value

Details

Generates a 3-panel plot for the Stalling Index data (Stalling Index, TSS, and gene body).

References

http://genomics.iit.it/groups/computational-epigenomics.html

Examples

  require(TxDb.Mmusculus.UCSC.mm9.knownGene)
  require(org.Mm.eg.db)
  txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
  isActiveSeq(txdb) <- c(rep(FALSE,18), TRUE, rep(FALSE, length(isActiveSeq(txdb))-19))
  # pointing to Pol2 BAM file
  # BAM file from the GEO GSM1234478 sample, limited to chr19:3200000-4000000
  Pol2bam <- system.file("extdata", "Pol2.bam", package="compEpiTools")
  # loading Pol2 peaks as a GRanges object
  # built based on the BED file from the GEO GSM1234478 sample
  # limited to chr19:3200000-4000000
  Pol2GR <- system.file("extdata", "Pol2GR.Rda", package="compEpiTools")
  load(Pol2GR)
  egs <- distanceFromTSS(Pol2GR, txdb=txdb)
  egs <- unique(egs$nearest_gene_id)
  SI_matrix <- stallingIndex(BAMlist=list(Pol2bam), peakGRlist=list(Pol2GR), 
    genesList=list(egs), transcriptDB=txdb, countMode='gene')
  plotStallingIndex(SI_matrix)
  restoreSeqlevels(txdb)