mCSEAPlot: Plot mCSEA results
In jordimartorell/mCSEA: Methylated CpGs Set Enrichment Analysis

Description Usage Arguments Value Author(s) See Also Examples

View source: R/mCSEAPlot.R

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

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"))

`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

'NULL'

Jordi Martorell Marugán, jordi.martorell@genyo.es

rankProbes, mCSEATest, mCSEAPlotGSEA

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)