methylKit Analysis

Read Bismark Coverage Files

library(methylKit)

file_list <- list('sample1.bismark.cov.gz', 'sample2.bismark.cov.gz',
                   'sample3.bismark.cov.gz', 'sample4.bismark.cov.gz')
sample_ids <- c('ctrl_1', 'ctrl_2', 'treat_1', 'treat_2')
treatment <- c(0, 0, 1, 1)  # 0 = control, 1 = treatment