README.md

In chanw0/MRS: Microbial Risk Score Framework

title: "MRS" output: html_document

```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE)

# MRS

Welcome to *MRS*'s page!


Installing *MRS*
-------------
To install the development version from github:

```r
library(devtools)
install_github("chanw0/MRS")

Once installed, the package can be loaded using:

library("MRS")

Examples

Example 1: Evaluation of MRS in terms of comparison between Healthy and Nonhealthy

1.1 using ANCOMBC method and Shannon index

```{r example1} discovery=GMHI[[1]]; validation=GMHI[[2]]; res=MRS(discovery, validation, GroupID="Group", DA.method="ancombc", measurement="shannon") AUC=res[[3]]

1.2 using ALDEx2 method and Shannon index

```{r example2}
res=MRS(discovery, validation, GroupID="Group", DA.method="ALDEx2", measurement="shannon")
AUC=res[[3]]

Example 2 Evaluation of MRS in terms of comparison between Healthy and a specific disease Healthy vs. CA

{r example3} discovery.sub=prune_samples(sample_data(discovery)$Group1 %in% c("Healthy","CA"),discovery) validation.sub=prune_samples(sample_data(validation)$Group1 %in% c("Healthy","CA"),validation) res=MRS(discovery.sub, validation.sub, GroupID="Group", DA.method="ALDEx2", measurement="shannon") AUC=res[[3]]

Development team

Authors/developers

MRS is developed by:

• Chan Wang
• Huilin Li

Maintainer

• Chan Wang
• Huilin Li

chanw0/MRS documentation built on Aug. 25, 2023, 3:29 a.m.