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