mCSEAIntegrate: Integrate methylation and expression

View source: R/mCSEAIntegrate.R

mCSEAIntegrateR Documentation

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, jordi.martorell@genyo.es

See Also

rankProbes, mCSEATest

Examples

data(precomputedmCSEA)
data(exprTest)

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

resultsInt


jordimartorell/mCSEA documentation built on Oct. 24, 2024, 4:44 a.m.