ComBat.step2: Perform the second step of ComBat
In ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

Description Usage Arguments Details Value

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.

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

`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.

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

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.

ASSIGN documentation built on Nov. 8, 2020, 8:29 p.m.