dmpFinder: Find differentially methylated positions

Description

Identify CpGs where methylation is associated with a continuous or categorical phenotype.

Usage

dmpFinder(dat, pheno, type = c("categorical", "continuous"), qCutoff = 1, shrinkVar = FALSE)

Arguments

dat

A MethylSet or a matrix.

pheno

The phenotype to be tested for association with methylation.

type

Is the phenotype '‘continuous’ or ‘categorical’?

qCutoff

DMPs with an FDR q-value greater than this will not be returned.

shrinkVar

Should variance shrinkage be used? See details.

Value

A table with one row per CpG.

Details

This function tests each genomic position for association between methylation and a phenotype. Continuous phenotypes are tested with linear regression, while an F-test is used for categorical phenotypes.

Variance shrinkage (shrinkVar=TRUE) is recommended when sample sizes are small (<10). the="" sample="" variances="" are="" squeezed="" by="" computing="" empirical="" bayes="" posterior="" means="" using="" limma package.

Examples

Run this code

if (require(minfiData)) {

grp <- pData(MsetEx)$Sample_Group
MsetExSmall <- MsetEx[1:1e4,] # To speed up the example
M <- getM(MsetExSmall, type = "beta", betaThreshold = 0.001)
dmp <- dmpFinder(M, pheno=grp, type="categorical")
sum(dmp$qval < 0.05, na.rm=TRUE)
head(dmp)

}