TraditR2: Traditional Filtering Rule 2

In PERFect: Permutation filtration for microbiome data

Description

This rule is adopted from Milici et al. (2016) that removes taxa with low abundance level. Specifically, it keeps taxa with abundance level higher than 0.001%. Then it further selects taxa that satisfy at least one of the following conditions: Present in at least one sample at a relative abundance higher than 1% of the reads of that sample, present in at least 2% of samples at a relative abundance higher than 0.1% for a given sample, present in at least 5% of samples at any abundance level.

Usage

TraditR2(X, Ab_min = 0.001)

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.
Ab_min	Numerical value, set to 0.001 by default. Throughout all samples, taxa with abundance 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 <- TraditR2(Counts)

PERFect documentation built on Nov. 8, 2020, 7:43 p.m.