Subsets a given list of CpGs by another list of CpGs

Source: R/accessory_funcs.R

Subsets a given list of CpGs by another list of CpGs

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

Value

List of column names and indexes

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.