read_hdf5_data: Writes values from input BED files into an in-disk...

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

Description

Writes values from input BED files into an in-disk HDF5Array

Usage

read_hdf5_data(
  files,
  ref_cpgs,
  col_list,
  batch_size = 20,
  n_threads = 1,
  h5_temp = NULL,
  zero_based = FALSE,
  strand_collapse = FALSE,
  verbose = TRUE
)

Arguments

files	list of strings; file.paths of BED files
ref_cpgs	data.table; list of CpG sites in the tab-delimited format of chr-start-end. Must be zero-based genome.
col_list	string; The column index object for the input BED files
batch_size	integer; The number of file to hold in memory at once
n_threads	integer; number of threads to use. Default 1. Be-careful - there is a linear increase in memory usage with number of threads. This option is does not work with Windows OS.
h5_temp	string; temporary directory to store hdf5
zero_based	boolean; flag for whether the input data is zero-based or not
strand_collapse	boolean; whether to collapse the crick strand into watson strand. Default FALSE
verbose	boolean; flag to output messages or not.

Details

Using the generated index for genomic coordinates, creates a NA-based dense matrtix of methylation values for each BED file/sample. Each column contains the meth. values for a single sample.

Value

List of HDF5Array. 1 is methylation, 2 is coverage. If no cov_idx is specified, 2 will be NULL

Examples

## Not run: 
#Do Nothing

## End(Not run)

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