mbecRBE: Remove Batch Effects (RBE)

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

Description

As part of the limma-package this method was designed to remove BEs from Microarray Data. The algorithm fits the full-model to the data, i.e., all relevant covariates whose effect should not be removed, and a model that only contains the known BEs. The difference between these models produces a residual matrix that (should) contain only the full-model-effect, e.g., treatment. As of now the mbecs-correction only uses the first input for batch-effect grouping. ToDo: think about implementing a version for more complex models.

Usage

mbecRBE(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.