aggregated_input: aggregated_input helper function

In rBiasCorrection: Correct Bias in DNA Methylation Analyses

aggregated_input helper function

Description

Internal function to present aggregated input data on which calculations are performed. This function does only have an effect, if repeated measurements are used for calibration a/o experimental data.

Usage

aggregated_input(
  datatable,
  description = c("experimental", "calibration"),
  vec_cal,
  type = NULL
)

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.
vec_cal	The vector containing the CpG columns (output of clean_dt with description = "calibration").
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).

Value

A data.table in the long format with aggregated means for each CpG site of each sample and the corresponding standard deviation.

Examples

experimental <- rBiasCorrection::example.data_experimental
calibration <- rBiasCorrection::example.data_calibration

vec_cal <- calibration$vec_cal

experimental_aggregated <- aggregated_input(
  datatable = experimental$dat,
  description = "experimental",
  vec_cal = vec_cal,
  type = 1
)
dim(experimental_aggregated)
class(experimental_aggregated)

calibration_aggregated <- aggregated_input(
  datatable = calibration$dat,
  description = "calibration",
  vec_cal = vec_cal
)
dim(calibration_aggregated)
class(calibration_aggregated)

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