taxa.meansdn: Summarize abundance by group

In metamicrobiomeR: Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI & Random Effects

Description

This function summarizes taxa/pathway abundance tables to provide mean, sd, count by groups.

Usage

taxa.meansdn(
  taxtab,
  sumvar,
  groupvar,
  percent.filter = 0.05,
  relabund.filter = 5e-05,
  othervar = "none"
)

Arguments

taxtab	taxa/pathway abundance table from phylum to species or any preferred highest taxa level.
sumvar	main variable for summary
groupvar	variable to be stratified.
percent.filter	prevalence threshold (the percentage of number of samples the taxa/pathway available). Default is 0.05.
relabund.filter	relative abundance threshold (the minimum of the average relative abundance for a taxa/pathway to be retained). Default is 0.00005.
othervar	vector of variables that are not abundance variables to be summarized. Default is "none".

Value

table of mean, sd, count by group.

Examples

#Load summary tables of bacterial taxa relative abundance from Bangladesh data
data(taxtab6)
taxa.meansdn.rm<-taxa.meansdn(taxtab=taxtab6,sumvar="bf",groupvar="age.sample")

metamicrobiomeR documentation built on Nov. 9, 2020, 5:06 p.m.