read_meth: Extract the relevant columns from the files

In Mamie/scDNAmClock: Epigenetic clock on scMethyl-seq data

Description

Extract the relevant columns from the files

Usage

read_meth(files, chr_idx, pos_idx, met_idx, id, coverage_idx = NULL,
  strand_idx = NULL, unmet_idx = NULL, deduplicate = T, header = T,
  sep = "\t")

Arguments

files	The path to tsv files for methylation status
chr_idx	The index of column for chromosome
pos_idx	The index of column for position
met_idx	The index of column for the number of methylated reads
id	The id to each file
coverage_idx	The index of column containing coverage; optional
strand_idx	The index of column containing strand; optional
unmet_idx	The index of column for the number of unmethylated reads
deduplicate	Whether to sum the reads for rows with the same genomic location
header	Whether to there is a header
sep	delimiter for methylation status file

Mamie/scDNAmClock documentation built on Aug. 20, 2019, 7 p.m.