mbecBMC: Batch Mean Centering (BMC)

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

Description

For known BEs, this method takes the batches, i.e., subgroup of samples within a particular batch, and centers them to their mean.

Usage

mbecBMC(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.