dada2: isShiftDenovo – R documentation

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isShiftDenovo

Identify sequences that are identical to a more abundant sequence up to an overall shift.

Description

This function is a wrapper around isShift for collections of unique sequences. Each unique sequence is evaluated against a set of "parents" drawn from the sequence collection that are more abundant than the sequence being evaluated.

Usage

isShiftDenovo(unqs, minOverlap = 20, flagSubseqs = FALSE, verbose = FALSE)

Arguments

`unqs`	(Required). A `uniques-vector` or any object that can be coerced into one with `getUniques`.
`minOverlap`	(Optional). A `numeric(1)`. Default is 20. Minimum overlap required to call something a shift.
`flagSubseqs`	(Optional). A `logical(1)`. Default is FALSE. Whether or not to flag strict subsequences as shifts.
`verbose`	(Optional). `logical(1)` indicating verbose text output. Default FALSE.

Value

logical of length the number of input unique sequences. TRUE if sequence is an exact shift of a more abundant sequence. Otherwise FALSE.

Examples

derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
dada1 <- dada(derep1, err=tperr1, errorEstimationFunction=loessErrfun, selfConsist=TRUE)
is.shift <- isShiftDenovo(dada1)
is.shift <- isShiftDenovo(dada1$denoised, minOverlap=50, verbose=TRUE)

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