topf {phyloseq} | R Documentation

## Make filter fun. that returns the top f fraction of taxa in a sample.

### Description

As opposed to `topp`, which gives the most abundant p fraction of observed taxa (richness, instead of cumulative abundance. Said another way, topf ensures a certain fraction of the total sequences are retained, while topp ensures that a certain fraction of taxa/species/OTUs are retained.

### Usage

    topf(f, na.rm=TRUE)

### Arguments

`f` | Single numeric value between 0 and 1.
`na.rm` | Logical. Should we remove NA values. Default `TRUE`.

### Value

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

### See Also

`topk`, `topf`, `topp`, `rm_outlierf`

### Examples

    t1 <- 1:10; names(t1)<-paste("t", 1:10, sep="")
    topf(0.6)(t1)
    ## 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(topf(0.4))
    (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 1.38.0 Index]