filter_features: Filter low abundance features from a table.

In jbisanz/qiime2R: qiime2R

Filter low abundance features from a table.

Description

Takes a table of features (samples are columns) and remove features that do not appear at in at least X samples OR do not have at least Y reads.

Usage

filter_features(features, minsamples, minreads, verbose)

Arguments

features	Table of feature/OTU/ASV counts where Samples are columns and feature IDs are row names
minsamples	A minimum number of samples (>=) for the feature/OTU/ASV to be observed in. (Default=2)
minreads	A minimum number of reads (>=) for a feature/OTU/ASV to be kept across all samples. (Default=2)
verbose	Should summary be printed? (T/F)

Value

filtered feature table

jbisanz/qiime2R documentation built on Dec. 17, 2024, 4:09 p.m.