batch_correction: Correction of batch effect in merged dataset

In madhulika-EBI/Batchevaluation: Toolkit for batch correction

Correction of batch effect in merged dataset

Description

This function performs various type of batch-correction on given merged dataset and output batch-corrected data as a list.

Arguments

experiment	It is the merged dataset obtained at the previous step ('merge_experiments').
model	A R formula mentioning the biological factor to take into account during the correction.
k	No. of confounders for RUV methods and denotes the "number of factors of unwanted variation to remove". If k is not provided it will then estimated from input data.
batch	meta-data column which has information about batch-label
filter	A string. Should be one of following string- 'symbol', 'ensembl_gene_id', or 'entrezgene_id' depending on gene label for the given dataset.

Details

This function contains a cocktail of various batch-correction methods.

For Microarray, 'batch_correction' function has following methods-

a) limma- Default limma setting, b) GFS - Gene Fuzzy Score method. c) Robust Quantile Normalization- quantile normalization method from PreprocessCore package, d) ComBat- Implemented from SVA package, e) Q_ComBat - It is Quantile+ parametric adjustment of ComBat, f) MNN - is default mnnCorrect function from batchelor package. g) naiveRandRUV_HK - default naiveRandRUV using Human HK genes from RUVnormalize package, h) Q_naiveRandRUV_HK - is Qunatile+ naiveRandRUV_HK, i) naiveRandRUV_empi.controls- default naiveRandRUV using empirically derived HK genes from RUVnormalize package, j) Q_naiveRandRUV_empi.controls - is Qunatile+ naiveRandRUV_empi.controls.

For bulk-RNAseq, 'batch_correction' function has following methods-

a) limma- default limma setting, b) ComBat- implemented from SVA package, c) ComBat_seq - implemented from ComBat-Seq package, d) MNN- default mnnCorrect function from batchelor package, e) RUVs- default RUVs function from RUVSeq package, g) scBatch- batch correction method implemented in scBatch package.

Value

A list of the batch-corrected experiment.

madhulika-EBI/Batchevaluation documentation built on Jan. 27, 2023, 5:27 p.m.