FirstFilter: This function is used for the first step of filtering which...

In MicrobiomeSurv: Biomarker Validation for Microbiome-Based Survival Classification and Prediction

This function is used for the first step of filtering which removes OTUs having all zeros (inactive OTUs). The input is an OTU matrix with rows are OTUs and columns are subjects.

Description

This function is used for the first step of filtering which removes OTUs having all zeros (inactive OTUs). The input is an OTU matrix with rows are OTUs and columns are subjects.

Usage

FirstFilter(Micro.mat)

Arguments

Micro.mat

A large or small microbiome matrix. A matrix with microbiome profiles where the number of rows should be equal to the number of taxa and number of columns should be equal to number of patients.

Value

A smaller microbiome matrix.

Micro.mat.trim

The OTU matrix after removing all inactive OTUs

Author(s)

Thi Huyen Nguyen, [e-mail]

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

FirstFilter

Examples

# Preparing data for analysis at OTU level
data(Week3_otu)
Week3_otu = data.frame(Week3_otu)
otu_mat_w3 = t(data.matrix(Week3_otu[ , 1:2720]))
colnames(otu_mat_w3) = Week3_otu$SampleID
# Filtering first step
otu_w3 = FirstFilter(Micro.mat = otu_mat_w3)

MicrobiomeSurv documentation built on Oct. 12, 2023, 9:06 a.m.