parse_source_idx: Subsets a given list of CpGs by another list of CpGs

In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Description

Subsets a given list of CpGs by another list of CpGs

Usage

parse_source_idx(
  chr_idx = NULL,
  start_idx = NULL,
  end_idx = NULL,
  strand_idx = NULL,
  beta_idx = NULL,
  M_idx = NULL,
  U_idx = NULL,
  cov_idx = NULL,
  verbose = TRUE
)

Arguments

chr_idx	integer; column of the chromosome
start_idx	integer; column of the CpG start site
end_idx	integer; column of the CpG end site
strand_idx	integer; column of the strand
beta_idx	integer; column of the beta value
M_idx	integer; column of the # of methylated reads
U_idx	integer; column of the # of unmethylated reads
cov_idx	integer; column of the coverage
verbose	flag to output messages or not

Details

Typically used to reduce the number of potential CpG sites to include only those present in the input files so as to maximize performance and minimize resources. Can also be used for quality control to see if there is excessive number of CpG sites that are not present in the reference genome.

Value

List of column names and indexes

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.