diffMeth {msgbsR} | R Documentation |
Determines differential methylated sites from a RangedSummarizedExperiment
diffMeth(se, cateogory, condition1, condition2, block = NULL, cpmThreshold, thresholdSamples)
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. |
A data frame containing which cut sites that are differenitally methylated.
Benjamin Mayne
# Load data data(ratdata2) top <- diffMeth(se = ratdata2, cateogory = "Group", condition1 = "Control", condition2 = "Experimental", cpmThreshold = 1, thresholdSamples = 1)