diffMeth: diffMeth

In msgbsR: msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions

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)

msgbsR documentation built on Nov. 8, 2020, 6:51 p.m.