Filter taxa based on abundance values per sample

filterTaxa filters the number of taxa per sample based on a minimum value of abundance. This functions works with both phyloseq and TreeSummarizedExperiment objects.

filterTaxa(x, min_ab = 1, min_per = 0.2)

Arguments

x

A phyloseq or TreeSummarizedExperiment object with otu_table/assay and sample_data/colData

min_ab

The minimum value of abundance for taxon to be considered as present in a sample. Default is 1. The default value of 1 could be good for counts. Relative abundance or other data transformations might require another threshold value.

min_per

minimum percentage of samples in which each taxon must be present in order to be kept in the data. Default is 0.2. Taxon presence is dtermined by the `min_ab` argument (see above).

Value

The filtered phyloseq/TreeSummarized object