ComBat.step2: Perform the second step of ComBat

In compbiomed/ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

Perform the second step of ComBat

Description

The first ComBat step (on the signatures only) has already been performed. This step performs batch correction on the test data, using reference batch ComBat, to prepare the test data for ASSIGN analysis.

Usage

ComBat.step2(
  testData,
  pcaPlots = FALSE,
  combat_train = NULL,
  plots_to_console = FALSE
)

Arguments

testData	The input test data to batch correct
pcaPlots	a logical value indicating whether or not the function should create PCA plots. The default is FALSE.
combat_train	the ComBat training data data frame. If you do not have this, the function will attempt to download it from the internet. Please contact the developers if you have any issues with access to the file.
plots_to_console	By default this function will write PDF versions of the plots. Set this to TRUE to send the plots to the command line. The default is FALSE.

Details

This function downloads the training data from the internet, so an internet connection is necessary

Value

A list of data.frames is returned, including control (GFP) and signature data, as well as the batch corrected test data. This data can go directly into the runassign.single and runassign.multi functions, or subsetted to go directly into ASSIGN.

compbiomed/ASSIGN documentation built on June 28, 2023, 4 a.m.