topk: Make filter fun. the most abundant 'k' taxa

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

Make filter fun. the most abundant k taxa

Description

Make filter fun. the most abundant k taxa

Usage

topk(k, na.rm=TRUE)

Arguments

k	An integer, indicating how many of the most abundant taxa should be kept.
na.rm	A logical. Should NAs be removed. Default is TRUE.

Value

Returns a function (enclosure) that will return TRUE for each element in the most abundant k values.

See Also

topk, topf, topp, rm_outlierf

Examples

## 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)

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.