getAllSampleMetaMethFreq: get average methylation frequency from all matrices

In jsemple19/methMatrix: Manipulate Lists of Methylation Matrices

get average methylation frequency from all matrices

Description

In order to do a metagene plot from matrices, the average methylation frequency from all matrices with more reads than minReads is collected into a data frame

Usage

getAllSampleMetaMethFreq(relCoordMats, samples, regionGRs, minReads = 10)

Arguments

relCoordMats	A table of paths to methylation matrices which have been converted to relative coordinates
samples	A list of samples to plot (same as sample names in relCoordMats)
regionGRs	A genomic regions object with all regions for which matrices should be extracted (same as in relCoordMats). The metadata columns must contain a column called "ID" with a unique ID for each region.
minReads	The minimal number of reads required in a matrix for average frequency to be calculated.

Value

Data frame with average methylation at relative coordinates extracted from all matrices for all samples

jsemple19/methMatrix documentation built on Aug. 19, 2022, 3:57 p.m.