metamicrobiomeR (version 1.2)

taxa.filter: Filter relative abundance data

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

# NOT RUN {
#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)
# }