Make filter fun. the most abundant k taxa
Make filter fun. the most abundant k taxa
topk(k, na.rm=TRUE)
k |
An integer, indicating how many of the most abundant taxa should be kept. |
na.rm |
A logical. Should |
Returns a function (enclosure) that will return TRUE for each element in the most abundant k values.
topk, topf,
topp, rm_outlierf
## Use simulated abundance matrix set.seed(711) testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE) f1 <- filterfun_sample(topk(2)) wh1 <- genefilter_sample(testOTU, f1, A=2) wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE) prune_taxa(wh1, testOTU) prune_taxa(wh2, testOTU)
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