MMINP.predict: Predict metabolites from new microbiome samples using MMINP...

In MMINP: Microbe-Metabolite Interactions-Based Metabolic Profiles Predictor

Predict metabolites from new microbiome samples using MMINP model.

Description

This function aims to predict potentially metabolites in new microbial community using trained MMINP model. If genes in model are not appear in newdata, then this procedure will fill them up with 0. Note that this function does not center or scale the new microbiome matrixs, you would better do preprocessing on newdata in advance.

Usage

MMINP.predict(model, newdata, minGeneSize = 0.5)

Arguments

model	List of class "mminp" or "o2m", produced by MMINP.train or o2m.
newdata	New matrix of microbial genes, each column represents a gene.
minGeneSize	A numeric between 0-1, minimal size of genes in model contained in newdata.

Details

The model must be class 'mminp' or 'o2m'. The column of newdata must be microbial genes.

Value

Predicted Data

Examples

data(MMINP_trained_model)
data(test_metag)
test_metag_preprocessed <- MMINP.preprocess(test_metag, normalized = FALSE)
pred_metab <- MMINP.predict(model = MMINP_trained_model$model,
newdata = test_metag_preprocessed)

MMINP documentation built on July 5, 2022, 1:08 a.m.