SummaryData: This function gives indices such as Observed richness,...

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

This function gives indices such as Observed richness, Shannon index, Inverse Simpson, ... of higher level such as levelily, order, phylum, ...

Description

This function gives indices such as Observed richness, Shannon index, Inverse Simpson, ... of higher level such as levelily, order, phylum, ...

Usage

SummaryData(Micro.mat, info, measure = "observed")

Arguments

Micro.mat	an OTU matrix with OTUs in rows and subjects in columns.
info	A n x 2 matrix containing a column of OTU's names and a column of the corresponding information of the chosen level.
measure	The indices at chosen level that user wishes to use. It can be observed richness, Shannon index, inverse Simpson, ...

Value

A matrix of the selected measurement of the chosen level.

level.measure

A matrix of measurements at levelily level of patients

Author(s)

Thi Huyen Nguyen, [e-mail]

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

SummaryData

Examples

# Read dataset
data(Week3_otu)
Week3_otu = data.frame(Week3_otu)
otu_mat_w3 = t(data.matrix(Week3_otu[ , 1:2720]))
data(fam_info_w3)

# USing the function
fam_shan_w3 = SummaryData(Micro.mat = otu_mat_w3, info = fam_info_w3, measure = "shannon")

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