topp {phyloseq} | R Documentation

## Make filter fun. that returns the most abundant `p` fraction of taxa

### Description

Make filter fun. that returns the most abundant `p` fraction of taxa

### Usage

    topp(p, na.rm=TRUE)

### Arguments

`p` | A numeric of length 1, indicating what fraction of the most abundant taxa should be kept.
`na.rm` | A logical. Should `NA`s be removed. Default is `TRUE`.

### Value

A function (enclosure), suitable for `filterfun_sample`, that will return `TRUE` for each element in the most abundant p fraction of taxa.

### 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)
    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)

[Package phyloseq version 1.24.2 Index]