export_beds: Exports all samples in an 'scMethrix' objects into individual...

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

Description

Exports all samples in an scMethrix objects into individual bedgraph files

Usage

export_beds(
  scm = NULL,
  path = NULL,
  suffix = NULL,
  include = FALSE,
  na.rm = TRUE,
  header = FALSE,
  verbose = TRUE
)

Arguments

scm	scMethrix; the single cell methylation experiment
path	string; the file.path of the directory to save the files
suffix	string; optional suffix to add to the exported bed files
include	boolean; flag to include the values of non-standard assays in the bedgraph file
na.rm	boolean; flag to remove the NA values from the output data
header	boolean; flag to add the header onto each column
verbose	boolean; Flag for outputting function status messages. Default = TRUE

Details

The structure of the bedgraph files will be a tab-deliminated structure of: Chromosome | CpG start site | CpG end site | methylation score | coverage | Additional assays (if include = TRUE)

If additional assays are used, and headers enabled, it is up to the user to ensure that assay names are not protected in any downstream analysis of the bedgraph files

Value

nothing

Examples

data('scMethrix_data')
export_beds(scMethrix_data,path=paste0(tempdir(),"/export"))

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