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 1.14.0 Index]