mCSEAPlot {mCSEA} | R Documentation

## Plot mCSEA results

### Description

Generate a graphic with the genomic context of the selected DMR, showing methylation status at each CpG site of different samples groups

### Usage

    mCSEAPlot(mCSEAResults, regionType, dmrName, extend = 1000,
      chromosome = TRUE, leadingEdge = TRUE, CGI = FALSE, genes = TRUE,
      transcriptAnnotation = "transcript", makePDF = TRUE,
      col = c("blue", "magenta", "green", "red", "black"))

### Arguments

`mCSEAResults` | The object generated by mCSEATest function
`regionType` | The region type to be represented. Must be one of "promoters", "genes", "CGI" or "custom"
`dmrName` | The DMR of interest to be represented (e.g. gene name, CGI name...)
`extend` | The number of base pairs to extend the plot around the DMR of interest (default = 1000 bp)
`chromosome` | If TRUE, represent the chromosome and genome axis
`leadingEdge` | If TRUE, represent the bars indicating if each CpG belongs to the mCSEA leading edge (green) or not (red)
`CGI` | If TRUE, represent the annotated CpG islands
`genes` | If TRUE, represent the annotated genes
`transcriptAnnotation` | Labels showed at the genes track. Must be one of "transcript" (default), "symbol", "gene", "exon" or "feature"
`makePDF` | If TRUE, save the plot in pdf format in the working directory. Otherwise, draw the plot in the active graphics window
`col` | Vector with colors to plot methylation in different groups

### Value

'NULL'

### Author(s)

Jordi Martorell Marugán, jordi.martorell@genyo.es

### See Also

`rankProbes`, `mCSEATest`, `mCSEAPlotGSEA`

### Examples

    library(mCSEAdata)
    data(mcseadata)
    ## Not run:
    myRank <- rankProbes(betaTest, phenoTest, refGroup = "Control")
    set.seed(123)
    myResults <- mCSEATest(myRank, betaTest, phenoTest,
    regionsTypes = "promoters", platform = "EPIC")

    ## End(Not run)
    data(precomputedmCSEA)
    mCSEAPlot(myResults, "promoters", "CLIC6",
    transcriptAnnotation = "symbol", makePDF = FALSE)

[Package mCSEA version 1.6.0 Index]