methy_to_edger: Convert NanoMethResult object to edgeR methylation matrix

In Shians/NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing

Convert NanoMethResult object to edgeR methylation matrix

Description

Convert NanoMethResult object to edgeR methylation matrix

Usage

methy_to_edger(methy, regions = NULL, out_folder = tempdir(), verbose = TRUE)

Arguments

methy	the NanoMethResult object or path to the methylation tabix file.
regions	the regions to calculate log-methylation ratios over. If left NULL, ratios will be calculated per site.
out_folder	the folder to store intermediate files. One file is created for each sample and contains columns "chr", "pos", "total" and "methylated".
verbose	TRUE if progress messages are to be printed

Value

a matrix compatible with the edgeR differential methylation pipeline

Examples

nmr <- load_example_nanomethresult()
edger_mat <- methy_to_edger(nmr)

Shians/NanoMethViz documentation built on Dec. 17, 2024, 8:56 a.m.