getUniques {dada2} | R Documentation

## Get the uniques-vector from the input object.

### Description

This function extracts the `uniques-vector` from several different data objects, including `dada-class` and `derep-class` objects, as well as `data.frame` objects that have both $sequence and $abundance columns. The return value is an integer vector named by sequence and valued by abundance. If the input is already in `uniques-vector` format, that same vector will be returned.

### Usage

    getUniques(object, collapse = TRUE, silence = FALSE)

### Arguments

`object` | (Required). The object from which to extract the `uniques-vector`.
`collapse` | (Optional). Default TRUE. Should duplicate sequences detected in `object` be collapsed together, thereby imposing uniqueness on non-unique input.
`silence` | (Optional). Default FALSE. Suppress reporting of the detection and merger of duplicated input sequences.

### Value

`integer`. An integer vector named by unique sequence and valued by abundance.

### Examples

    derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
    dada1 <- dada(derep1, err=tperr1)
    getUniques(derep1)[1:3]
    getUniques(dada1)[1:3]
    getUniques(dada1$clustering)[1:3]

[Package dada2 version 1.14.1 Index]