Make filter fun. that returns the most abundant p fraction of taxa
Make filter fun. that returns the most abundant p fraction of taxa
topp(p, na.rm=TRUE)
p |
A numeric of length 1, indicating what fraction of the most abundant taxa should be kept. |
na.rm |
A logical. Should |
A function (enclosure), suitable for filterfun_sample,
that will return TRUE
for each element in the most abundant p fraction of taxa.
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) sample_sums(testOTU) f1 <- filterfun_sample(topp(0.2)) (wh1 <- genefilter_sample(testOTU, f1, A=1)) wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE) prune_taxa(wh1, testOTU) prune_taxa(wh2, testOTU)
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