Determine if input sequence is a bimera of putative parent sequences.

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Description

This function attempts to find an exact bimera of the parent sequences that matches the input sequence. A bimera is a two-parent chimera, in which the left side is made up of one parent sequence, and the right-side made up of a second parent sequence. If an exact bimera is found TRUE is returned, otherwise FALSE. Bimeras that are one-off from exact are also identified if the allowOneOff argument is TRUE.

Usage

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isBimera(sq, parents, allowOneOff = TRUE, minOneOffParentDistance = 4,
  maxShift = 16)

Arguments

sq

(Required). A character(1). The sequence being evaluated as a possible bimera.

parents

(Required). Character vector. A vector of possible "parent" sequence that could form the left and right sides of the bimera.

allowOneOff

(Optional). A logical(1). Default is TRUE. If TRUE, sq will be identified as a bimera if it is one mismatch or indel away from an exact bimera.

minOneOffParentDistance

(Optional). A numeric(1). Default is 4. Only sequences with at least this many mismatches to sq are considered as possible "parents" when flagging one-off bimeras. There is no such screen when identifying exact bimeras.

maxShift

(Optional). A numeric(1). Default is 16. Maximum shift allowed when aligning sequences to potential "parents".

Value

logical(1). TRUE if sq is a bimera of two of the parents. Otherwise FALSE.

See Also

isBimeraDenovo, removeBimeraDenovo

Examples

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derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
sqs1 <- getSequences(derep1)
isBimera(sqs1[[20]], sqs1[1:10])

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