getSequences: Get vector of sequences from input object.

Description Usage Arguments Value Examples

View source: R/misc.R

Description

This function extracts the unique 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 file.

Usage

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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

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


dada2 documentation built on May 20, 2017, 9:15 p.m.
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