adjust_EB: Perform batch adjustment on standardized feature abundances,...

In biobakery/MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

Perform batch adjustment on standardized feature abundances, based on EB shrinked per-batch location and scale parameters

Description

Perform batch adjustment on standardized feature abundances, based on EB shrinked per-batch location and scale parameters

Usage

adjust_EB(s_data, l_params_shrink, l_stand_feature, batchmod, n_batch,
  l_ind)

Arguments

s_data	feature-by-sample matrix of standardized abundances.
l_params_shrink	list of shrinked parameters, as returned by fit_shrink.
l_stand_feature	list of per-feature standardization fits, as returned by fit_stand_feature.
batchmod	design matrix for batch variables.
n_batch	number of batches in the data.
l_ind	list of indicator matrices, as returned by construct_ind.

Value

feature-by-sample matrix of batch-adjusted feature abundances.

biobakery/MMUPHin documentation built on March 30, 2024, 4:50 a.m.