TraditR1: Traditional Filtering Rule 1

In katiasmirn/PERFect: Permutation filtration for microbiome data

Description

This rule suggests to remove taxa that are mostly absent in all samples.

Usage

TraditR1(X, thresh =5)

Arguments

X	OTU COUNTS table, where taxa are columns and samples are rows of the table. It should be a in data frame format with columns corresponding to taxa names.
thresh	Numerical value, set to 5 by default. Throughout all samples, taxa that are present for less than this threshold with be removed.

Value

filtX

Filtered OTU table

Author(s)

Ekaterina Smirnova

References

Smirnova, E., Huzurbazar, H., Jafari, F. “PERFect: permutation filtration of microbiome data.

Examples

data(mock2)

# Counts data matrix
Counts <- mock2$Counts

# Filtering
Filtered_X <- TraditR1(Counts)

katiasmirn/PERFect documentation built on Sept. 17, 2019, 11:54 a.m.