TraditR2 {PERFect} | R Documentation |
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.
TraditR2(X, Ab_min = 0.001)
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. |
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 <- TraditR2(Counts)