taxa.filter: Filter relative abundance data

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

Description

This function filters bacterial taxa or pathway relative abundance tables based on the percentage of samples with their availability (prevalence) and relative abundance thresholds. It will remove taxa/pathway with relative abundance <relabund.filter and available in <percent.filter of number of samples.

Usage

taxa.filter(taxtab, percent.filter = 0.05, relabund.filter = 5e-05)

Arguments

taxtab	taxa/pathway relative abundance table.
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.

Value

list of all taxa/pathways retained after filtering.

Examples

#Load summary tables of bacterial taxa relative abundance from Bangladesh data
data(taxtab6)
taxlist.rm<-taxa.filter(taxtab=taxtab6,percent.filter = 0.05,
relabund.filter = 0.00005)

Example output

Loading required package: gamlss
Loading required package: splines
Loading required package: gamlss.data

Attaching package: ‘gamlss.data’

The following object is masked from ‘package:datasets’:

    sleep

Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.2-0  ********** 
For more on GAMLSS look at https://www.gamlss.com/
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metamicrobiomeR documentation built on Nov. 9, 2020, 5:06 p.m.