diffMeth {msgbsR} | R Documentation

## diffMeth

### Description

Determines differential methylated sites from a RangedSummarizedExperiment

### Usage

    diffMeth(se, cateogory, condition1, condition2,
                     block = NULL, cpmThreshold, thresholdSamples)

### Arguments

`se` | A RangedSummarizedExperiment containing meta data of the samples.
`cateogory` | The heading name in the sample data to be tested for differential methylation.
`condition1` | The reference group within the cateogory.
`condition2` | The experimental group within the cateogory.
`block` | The heading name in the sample data if differential methylation is to be tested with a blocking factor. Default is NULL.
`cpmThreshold` | Counts per million threshold of read counts to be filtered out of the analysis.
`thresholdSamples` | Minimum number of samples to contain the counts per million threshold.

### Value

A data frame containing which cut sites that are differenitally methylated.

### Author(s)

Benjamin Mayne

### Examples

    # Load data
    data(ratdata2)
    top <- diffMeth(se = ratdata2, cateogory = "Group",
           condition1 = "Control", condition2 = "Experimental",
           cpmThreshold = 1, thresholdSamples = 1)

[Package msgbsR version 1.12.0 Index]