threshrank {phyloseq} | R Documentation

## Thresholded rank transformation.

### Description

The lowest `thresh` values in `x` all get the value 'thresh'.

### Usage

    threshrank(x, thresh, keep0s=FALSE, ...)

### Arguments

`x` | (Required). Numeric vector to transform.
`thresh` | A single numeric value giving the threshold.
`keep0s` | A logical determining whether 0's in `x` should remain a zero-value in the output. If FALSE, zeros are treated as any other value.
`...` | Further arguments passes to the `rank` function.

### Value

A ranked, (optionally) thresholded numeric vector with length equal to `x`. Default arguments to `rank` are used, unless provided as additional arguments.

### See Also

`transform_sample_counts`, `rank`, `threshrankfun`

### Examples

    #
    (a_vector <- sample(0:10, 100, TRUE))
    threshrank(a_vector, 5, keep0s=TRUE)
    data(GlobalPatterns)
    GP <- GlobalPatterns
    ## These three approaches result in identical otu_table
    (x1 <- transform_sample_counts( otu_table(GP), threshrankfun(500)) )
    (x2 <- otu_table(apply(otu_table(GP), 2, threshrankfun(500)), taxa_are_rows(GP)) )
    identical(x1, x2)
    (x3 <- otu_table(apply(otu_table(GP), 2, threshrank, thresh=500), taxa_are_rows(GP)) )
    identical(x1, x3)

[Package phyloseq version 1.38.0 Index]