PerformRNAseqDE: Main function to perform RNAseq analysis

In xia-lab/MicrobiomeAnalystR: MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.

Main function to perform RNAseq analysis

Description

This functions performs RNAseq analysis on the microbiome data.

Usage

PerformRNAseqDE(mbSetObj, opts, p.lvl, variable, shotgunid, taxrank)

Arguments

mbSetObj	Input the name of the mbSetObj.
opts	Character, input "EdgeR" to use the edgeR algorithm and "DESeq2" to use the DESeq2 algorithm.
p.lvl	Numeric, input the adjusted p-value cutoff.
variable	Character, input the experimental factor.
shotgunid	Only valid for SDP module, set to "NA".
taxrank	Character, input the taxonomic level to use for RNAseq analysis.
datatype	Character, input "16S" if the data is marker gene data and "metageno" if it is metagenomic data.

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MicrobiomeAnalystR documentation built on April 17, 2024, 7:45 p.m.