clean_dt: clean_dt helper function

In rBiasCorrection: Correct Bias in DNA Methylation Analyses

clean_dt helper function

Description

Internal function, that checks the formatting of imported files and prepares them to be applicable for the following pcr-bias correction steps.

Usage

clean_dt(
  datatable,
  description = c("calibration", "experimental"),
  type = 1L,
  logfilename
)

Arguments

datatable	A data.table object that contains either the experimental data or the calibration data.
description	A character string, indicating if datatable contains either "calibration" data or "experimental" data.
type	A single integer. Type of data to be corrected: either 1L (one locus in many samples, e.g. pyrosequencing data) or 2L (many loci in one sample, e.g. next-generation sequencing data or microarray data).
logfilename	A character string. Path to a file to save the log messages (default = paste0(tempdir(), "/log.txt")).

Value

If a valid file is provided, the function returns a cleaned data.table, suited for BiasCorrection.

Examples

logfilename <- paste0(tempdir(), "/log.txt")
cleaned_experimental <- clean_dt(
  datatable = rBiasCorrection::example.data_experimental$dat,
  description = "experimental",
  type = 1,
  logfilename = logfilename
)
dim(cleaned_experimental)
class(cleaned_experimental)

rBiasCorrection documentation built on April 12, 2025, 1:16 a.m.