mCSEAIntegrate: Integrate methylation and expression

In jordimartorell/mCSEA: Methylated CpGs Set Enrichment Analysis

Integrate methylation and expression

Description

Uses mCSEA methylation analysis results and expression values to search for significant correlations between DMRs methylation and close genes expression.

Usage

mCSEAIntegrate(mCSEAResults, exprData, regionType = c("promoters", "genes",
  "CGI", "custom"), geneIDs = "SYMBOL", dmrName = NULL, pcutoff = 0.05,
  minCor = 0.5, minP = 0.05, makePlot = TRUE, folder = ".", nproc = 1)

Arguments

mCSEAResults	The object generated by mCSEATest function
exprData	A matrix or data frame with genes in rows and samples in columns. A SummarizedExperiment object can be used too
regionType	The region types to be represented. Must be one or more of "promoters", "genes", "CGI" and "custom"
geneIDs	Gene identifiers used in exprData. One of "SYMBOL", "ENSEMBL", "ENTREZID", "GENEID", "REFSEQ" or "UNIGENE"
dmrName	The DMR of interest to correlate with expression (e.g. gene name, CGI name...). If NULL (default), all DMRs with P-Value < pcutoff are selected
pcutoff	P-Value threshold to select DMRs if dmrName = NULL
minCor	Correlation threshold to output the results
minP	Correlation P-Value threshold to output the results
makePlot	If TRUE, generate corelation and save them in the folder specified by folder parameter
folder	Directory to save the correlation plots if makePlot = TRUE
nproc	Number of processors to be used

Value

A data.frame with the integration results.

Author(s)

Jordi Martorell Marugán, [e-mail]

See Also

rankProbes, mCSEATest

Examples

data(precomputedmCSEA)
data(exprTest)

resultsInt <- mCSEAIntegrate(myResults, exprTest, "promoters", "ENSEMBL",
                            "GATA2", makePlot = FALSE)

resultsInt

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