Parses BED files for methylation values using previously generated index genomic coordinates

read_bed_by_index(
  files,
  ref_cpgs = NULL,
  col_list = NULL,
  zero_based = FALSE,
  strand_collapse = FALSE,
  fill = TRUE
)

Arguments

files	string; file.paths of BED files to parse to parse
ref_cpgs	data.table; The index of all unique coordinates from the input BED files
col_list	string; The column index object for the input BED files
zero_based	boolean; Whether the input data is 0 or 1 based
strand_collapse	boolean; Default FALSE
fill	boolean; Fill the output matrix to match the ref_cpgs. This must be used for HDF5 input formats to ensure consistent spacing for the grid. It is optional for in-memory formats.

data.table containing vector of all indexed methylation values for the input BED

Creates an NA-based vector populated with methlylation values from the input BED file in the respective indexed genomic coordinates

if (FALSE) {
#Do Nothing
}