Description Usage Arguments Value Examples
A custom interface to FastqStreamer
for dereplicating amplicon sequences from fastq or compressed fastq files,
while also controlling peak memory requirement to support large files.
1 | derepFastq(fls, n = 1e+06, verbose = FALSE, qualityType = "Auto")
|
fls |
(Required). |
n |
(Optional). |
verbose |
(Optional). Default FALSE.
If TRUE, throw standard R |
qualityType |
(Optional). |
A derep-class
object or list of such objects.
1 2 3 4 5 | # Test that chunk-size, `n`, does not affect the result.
testFastq = system.file("extdata", "sam1F.fastq.gz", package="dada2")
derep1 = derepFastq(testFastq, verbose = TRUE)
derep1.35 = derepFastq(testFastq, n = 35, verbose = TRUE)
all.equal(getUniques(derep1), getUniques(derep1.35)[names(getUniques(derep1))])
|
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