CorrectBatchEffect: The CorrectBatchEffect function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The CorrectBatchEffect function

Description

top-level wrapper function for batch correction.

Usage

CorrectBatchEffect(
  GEN_Data,
  BatchData,
  batch.correction.method,
  MinInBatch = 5,
  featurePerSet = 50000
)

Arguments

GEN_Data	matrix with methylation.data or gene.expression.data with genes in rows and samples in columns
BatchData	dataframe with two columns: the first column indicates the sample names, and the second column indicates the batch ids.
batch.correction.method	character string. Should be either 'Seurat' or 'Combat'.
MinInBatch	integer indicating the batch size threshold. Batches smaller than this threshold will be removed. Default: 5
featurePerSet	integer indicating the row numbers to split the GEN_Data into small subsets. Default: 50,000

Details

(1) filters the batch data and the molecular data to keep only the overlapped samples. (2) removes extremely small batches. (3) if the molecular data have over 50,000 features (rows), it splits the data into subsets, with 50,000 features in each subset, and perform batch correction on each subset. (4) identify overlapped samples in batch corrected subsets, and merge the subsets into one matrix.

Value

matrix with corrected data

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.