Create Artificial Chimeras

Description

Creates artificial random chimeras from a set of sequences.

Usage

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CreateChimeras(myDNAStringSet,
               numChimeras = 10,
               numParts = 2,
               minLength = 80,
               maxLength = Inf,
               minChimericRegionLength = 30,
               randomLengths = TRUE,
               includeParents = TRUE,
               processors = 1,
               verbose = TRUE)

Arguments

myDNAStringSet

A DNAStringSet object with aligned sequences.

numChimeras

Number of chimeras desired.

numParts

Number of chimeric parts from which to form a single chimeric sequence.

minLength

Minimum length of the complete chimeric sequence.

maxLength

Maximum length of the complete chimeric sequence.

minChimericRegionLength

Minimum length of the chimeric region of each sequence part.

randomLengths

Logical specifying whether to create random length chimeras in addition to random breakpoints.

includeParents

Whether to include the parents of each chimera in the output.

processors

The number of processors to use, or NULL to automatically detect and use all available processors.

verbose

Logical indicating whether to display progress.

Details

Forms a set of random chimeras from the input set of (typically good quality) sequences. The chimeras are created by merging random sequences at random breakpoints. These chimeras can be used for testing the accuracy of the FindChimeras or other chimera finding functions.

Value

A DNAStringSet object containing chimeras. The names of the chimeras are specified as "parent #1 name [chimeric region] (distance from parent to chimera), ...".

If includeParents = TRUE then the parents of the chimeras are included at the end of the result. The parents are trimmed to the same length as the chimera if randomLengths = TRUE. The names of the parents are specified as "parent #1 name [region] (distance to parent #2, ...)".

Author(s)

Erik Wright DECIPHER@cae.wisc.edu

See Also

FindChimeras, Seqs2DB

Examples

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db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
dna <- SearchDB(db)
chims <- CreateChimeras(dna)
BrowseSeqs(chims)

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