normalizeDataComBat: Do ComBat normalization based on batch.

In uit-bdps/pippeline: Pipeline for processing high-dimensional multi-omics biobank datasets

Description

Do ComBat normalization based on batch using sva library.

Usage

normalizeDataComBat(data.new, bTabName, sampleID, batchVar)

Arguments

data.new	lumi object where colnames(data)=sample IDs and rownames(data) = probe IDs
bTabName	name of the table, which is used for extracting batch variable
sampleID	name of column in data.new dataframe, which represents sample ID number
batchVar	batch variable, i.e. vector formed from dataset, which gives batch parameter for ComBat

Value

normalized matrix where colnames(data)=sample IDs and rownames(data) = probe IDs

uit-bdps/pippeline documentation built on May 22, 2019, 5:35 p.m.