getSequences {dada2} | R Documentation

## Get vector of sequences from input object.

### Description

This function extracts the sequences from several different data objects, including including `dada-class` and `derep-class` objects, as well as `data.frame` objects that have both $sequence and $abundance columns. This function wraps the `getUniques` function, but return only the names (i.e. the sequences). Can also be provided the file path to a fasta or fastq file, a taxonomy table, or a DNAStringSet object. Sequences are coerced to upper-case characters.

### Usage

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

### Arguments

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

### Value

`character`. A character vector of the sequences.

### Examples

    derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
    dada1 <- dada(derep1, err=tperr1)
    getSequences(derep1)[1:5]
    getSequences(dada1)[1:5]
    getSequences(dada1$clustering)[1:5]

[Package dada2 version 1.16.0 Index]