PerformCategoryComp: Function to perform categorical comparison.

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

Function to perform categorical comparison.

Description

This functions performs categorical comparisons.

Usage

PerformCategoryComp(
  mbSetObj,
  taxaLvl,
  method,
  distnm,
  variable,
  covariates = FALSE,
  cov.vec = NA,
  model.additive = TRUE
)

Arguments

mbSetObj	Input the name of the mbSetObj.
taxaLvl	Input the name of the taxonomic level to calculate Beta-diversity comparison.
method	Statistical method to calculate beta-diversity significance. Use "adonis" for Permutational MANOVA, "anosim" for Analysis of Group Similarities and "permdisp" for Homogeneity of Group Dispersions.
distnm	Character, input the name of the distance method. "bray" for Bray-Curtis Index, "jsd" for Jensen-Shannon Divergence, "jaccard" for Jaccard Index, "unifrac" for Unweighted Unifrac Distance and "wunifrac" for Weighted Unifrac Distance.
variable	Input the name of the experimental factor to group the samples.
covariates	Boolean. TRUE to consider covariates, FALSE to only consider the main effect. Only valid for PERMANOVA.
cov.vec	Character vector. Input the names of the covariates to consider in the PERMANOVA model.
model.additive	Boolean. If TRUE, the model will be additive (i.e. data ~ var1 + var2), making the assumption that the two factor variables are independent. However, if FALSE, the model will consider the synergistic effects of the variables - interaction (i.e. data ~ var1*var2). "Different explanatory variables the effects on the outcome of a change in one variable may either not depend on the level of the other variable (additive model) or it may depend on the level of the other variable (interaction model)."

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.