FL_J {PERFect} | R Documentation |
This function calculates filtering loss due to removing a group of J taxa.
FL_J(X, J)
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. |
FL Filtering loss value.
Ekaterina Smirnova
Smirnova, E., Huzurbazar, H., Jafari, F. “PERFect: permutation filtration of microbiome data", to be submitted.
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)