topk {phyloseq} | R Documentation

## 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 `NA`s 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)

[Package phyloseq version 1.28.0 Index]