PerformLefseAnal: Main function to perform LEfSe analysis

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

Main function to perform LEfSe analysis

Description

This functions performs LEfSe analysis on the microbiome data.

Usage

PerformLefseAnal(
  mbSetObj,
  p.lvl,
  pvalOpt = "fdr",
  lda.lvl,
  variable,
  isfunc,
  shotgunid,
  taxrank
)

Arguments

mbSetObj	Input the name of the mbSetObj.
p.lvl	Numeric, input the adjusted p-value cutoff.
lda.lvl	Numeric, input the Log LDA score cutoff.
variable	Character, input the name of the experimental factor.
isfunc	Logical, default set to "F".
shotgunid	Only valid for SDP module, set to "NA".
taxrank	Character, input the taxonomic level to perform univariate analysis.
datatype	Character, input whether the data is marker gene data ("16S") or metagenomic data ("metageno").

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.