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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/misc.R
\name{getSequences}
\alias{getSequences}
\title{Get vector of sequences from input object.}
\usage{
getSequences(object, collapse = FALSE, silence = TRUE)
}
\arguments{
\item{object}{(Required). The object from which to extract the sequences.}
\item{collapse}{(Optional). Default FALSE.
Should duplicate sequences detected in \code{object} be collapsed together, thereby
imposing uniqueness on non-unique input.}
\item{silence}{(Optional). Default TRUE.
Suppress reporting of the detection and merger of duplicated input sequences.}
}
\value{
\code{character}. A character vector of the sequences.
}
\description{
This function extracts the sequences from several different data objects, including
including \code{\link{dada-class}} and \code{\link{derep-class}} objects, as well as
\code{data.frame} objects that have both $sequence and $abundance columns. This function
wraps the \code{\link{getUniques}} function, but return only the names (i.e. the sequences).
Can also be provided the file path to a fasta or fastq file, a taxonomy table, or a
DNAStringSet object. Sequences are coerced to upper-case characters.
}
\examples{
derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
dada1 <- dada(derep1, err=tperr1)
getSequences(derep1)[1:5]
getSequences(dada1)[1:5]
getSequences(dada1$clustering)[1:5]
}
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