read_bed_by_index: Parses BED files for methylation values using previously...

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

Description

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

Usage

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.

Details

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

Value

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

Examples

## Not run: 
#Do Nothing

## End(Not run)

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