mbecBat: Combat Batch Effects (ComBat)

In buschlab/MBECS: Evaluation and correction of batch effects in microbiome data-sets

Description

This method uses an non-/parametric empirical Bayes framework to correct for BEs. Described by Johnson et al. 2007 this method was initially conceived to work with gene expression data and is part of the sva-package in R.

Usage

mbecBat(input.obj, model.vars, type = "clr")

Arguments

input.obj	phyloseq object or numeric matrix (correct orientation is handeled internally)
model.vars	Vector of covariate names. First element relates to batch.
type	Which abundance matrix to use, one of 'otu, tss, clr'. DEFAULT is 'clr'.

Details

The input for this function is supposed to be an MbecData object that contains total sum-scaled and cumulative log-ratio transformed abundance matrices. Output will be a matrix of corrected abundances.

Value

A matrix of batch-effect corrected counts

buschlab/MBECS documentation built on Jan. 21, 2022, 1:27 a.m.