mCSEAPlot: Plot mCSEA results

In jordimartorell/mCSEA: Methylated CpGs Set Enrichment Analysis

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, [e-mail]

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)

jordimartorell/mCSEA documentation built on Dec. 8, 2024, 10:32 a.m.