plotStallingIndex {compEpiTools} | R Documentation

## 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

### Details

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

### Value

A plot

### 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)

[Package compEpiTools version 1.21.1 Index]