dada2: isPhiX – R documentation

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isPhiX

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.

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)

dada2

Accurate, high-resolution sample inference from amplicon sequencing data

v1.18.0

LGPL-3

Authors

Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes

Initial release

2020-08-07