RomicsBatchCorrection: romicsBatchCorrection()

In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines

romicsBatchCorrection()

Description

Performs the sva::ComBat() batch correction on the data layer of the romics_object. The data layer must not contain missing values and the factor utilized will be the one used for the correction.

Usage

romicsBatchCorrection(
  romics_object,
  batch_factor = "factor",
  method = "ComBat",
  ...
)

Arguments

romics_object	A romics_object created using romicsCreateObject()
batch_factor	has to be a factor contained in the romics_object that will serve as batch covariate To obtain the
method	has to be either 'ComBat' or 'mean.only' to indicate how the ComBat function should be run.
...	parameters can be passed to sva::ComBat(), see sva::ComBat() documentation for more details.

Details

This function is used to perform a ComBat batch correction on a romics_object. it can be performed using the ComBat method or using a mean.only method. sva::ComBat() documentation for more details.

Value

This function returns a transformed romics_object.

Author(s)

Geremy Clair

PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.