Description Usage Arguments Value Examples
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 $abundance columns. This function
wraps the getUniques
function, but return only the names (i.e. the sequences).
Can also be provided the file path to a fasta or fastq file, a taxonomy table, or a
DNAStringSet object. Sequences are coerced to upper-case characters.
1 | getSequences(object, collapse = FALSE, silence = TRUE)
|
object |
(Required). The object from which to extract the sequences. |
collapse |
(Optional). Default FALSE.
Should duplicate sequences detected in |
silence |
(Optional). Default TRUE. Suppress reporting of the detection and merger of duplicated input sequences. |
character
. A character vector of the sequences.
1 2 3 4 5 | derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
dada1 <- dada(derep1, err=tperr1)
getSequences(derep1)[1:5]
getSequences(dada1)[1:5]
getSequences(dada1$clustering)[1:5]
|
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