ApplyAbundanceFilter: Function to filter uploaded data

Description Usage Arguments Author(s)

View source: R/general_proc.R

Description

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

Usage

1
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 [email protected] McGill University, Canada License: GNU GPL (>= 2)


xia-lab/MicrobiomeAnalystR documentation built on March 14, 2020, 4:44 a.m.