getSequences: Get vector of sequences from input object.

In benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data

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]

benjjneb/dada2 documentation built on Dec. 5, 2024, 4:02 p.m.