FL_J {PERFect}R Documentation

Filtering Loss for a set of filtered taxa J

Description

This function calculates filtering loss due to removing a group of J taxa.

Usage

FL_J(X, J)

Arguments

X

OTU 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.

J

A vector of J taxa to be removed. It must be subset of column names of X.

Value

FL Filtering loss value.

Author(s)

Ekaterina Smirnova

References

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

See Also

FiltLoss

Examples

data(mock2)

# Proportion data matrix
Prop <- mock2$Prop

# Counts data matrix
Counts <- mock2$Counts

#arrange counts in order of increasing number of samples taxa are present in
NP <- NP_Order(Counts)
Counts <- Counts[,NP]

# Extract the taxa names to be removed
J <- colnames(Counts)[1:30]

#Calculate filtering loss due to removing these taxa
FL_J(Counts,J)


[Package PERFect version 1.6.0 Index]