rm_outlierf {phyloseq} | R Documentation

## Set to FALSE any outlier species greater than f fractional abundance.

### Description

This is for removing overly-abundant outlier taxa, not for trimming low-abundance taxa.

### Usage

    rm_outlierf(f, na.rm=TRUE)

### Arguments

`f` | Single numeric value between 0 and 1. The maximum fractional abundance value that a taxa will be allowed to have in a sample without being marked for trimming.
`na.rm` | Logical. Should we remove NA values. Default `TRUE`.

### Value

A function (enclosure), suitable for `filterfun_sample`.

### See Also

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

### Examples

    t1 <- 1:10; names(t1)<-paste("t", 1:10, sep="")
    rm_outlierf(0.15)(t1)
    ## Use simulated abundance matrix
    set.seed(711)
    testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE)
    taxa_sums(testOTU)
    f1  <- filterfun_sample(rm_outlierf(0.1))
    (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 1.30.0 Index]