mCSEAPlot {mCSEA} | R Documentation |
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)
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 |
'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)