isPhiX {dada2} | R Documentation

## Determine if input sequence(s) match the phiX genome.

### Description

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.

### Usage

    isPhiX(seqs, wordSize = 16, minMatches = 2, nonOverlapping = TRUE, ...)

### Arguments

`seqs` | (Required). A `character` vector of A/C/G/T sequences.
`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.

### Value

`logical(1)`. TRUE if sequence matched the phiX genome.

### See Also

`fastqFilter`, `fastqPairedFilter`

### Examples

    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)

[Package dada2 version 1.20.0 Index]