TraditR1 {PERFect} | R Documentation |
This rule suggests to remove taxa that are mostly absent in all samples.
TraditR1(X, thresh =5)
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. |
filtX |
Filtered OTU table |
Ekaterina Smirnova
Smirnova, E., Huzurbazar, H., Jafari, F. “PERFect: permutation filtration of microbiome data.
data(mock2) # Counts data matrix Counts <- mock2$Counts # Filtering Filtered_X <- TraditR1(Counts)