isShiftDenovo: Identify sequences that are identical to a more abundant...

In benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data

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.

See Also

isBimera

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)

benjjneb/dada2 documentation built on Dec. 5, 2024, 4:02 p.m.