Description Usage Arguments Value See Also Examples
This function compares the word-profile of the input sequences to the phiX genome, and the reverse complement of the phiX genome. If enough exactly matching words are found, the sequence is flagged.
1 |
seqs |
(Required). A |
wordSize |
(Optional). Default 16. The size of the words to use for comparison. |
minMatches |
(Optional). Default 2. The minimum number of words in the input sequences that must match the phiX genome (or its reverse complement) for the sequence to be flagged. |
nonOverlapping |
(Optional). Default TRUE. If TRUE, only non-overlapping matching words are counted. |
... |
(Optional). Ignored. |
logical(1)
.
TRUE if sequence matched the phiX genome.
fastqFilter
, fastqPairedFilter
1 2 3 4 | derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
sqs1 <- getSequences(derep1)
is.phi <- isPhiX(sqs1)
is.phi <- isPhiX(sqs1, wordSize=20, minMatches=1)
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