ApplyAbundanceFilter: Function to filter uploaded data

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

Function to filter uploaded data

Description

This function filters data based on low counts in high percentage samples. Note, first is abundance, followed by variance.

Usage

ApplyAbundanceFilter(mbSetObj, filt.opt, count, smpl.perc)

Arguments

mbSetObj	Input the name of the mbSetObj.
filt.opt	Character, input the low count filter option. "prevalence" to filter based on prevalence in samples, "mean" to filter by the mean abundance value, and "median" to filter by median abundance value.
count	Numeric, input the minimum count. Set to 0 to disable the low count filter.
smpl.perc	Numeric, input the percentage of samples for which to filter low counts.

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.