dmpFinder {minfi} | R Documentation

## 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.

### 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 the limma package.

### Value

A table with one row per CpG.

### Author(s)

Martin Aryee aryee@jhu.edu.

### See Also

`squeezeVar` and the limma package in general.

### Examples

    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)

    }

[Package minfi version 1.28.4 Index]