prepareMlgtRun-methods: Prepare to run mlgt
In mlgt: Multi-Locus Geno-Typing

Description Usage Arguments Details Value See Also

Required before mlgt is used. Create BLAST databases and assign sequences using BLAST.

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  prepareMlgtRun(designObject, projectName, runName,
    samples, markers, fTags, rTags, inputFastaFile,
    overwrite)

`designObject`	Only used internally.
`projectName`	In which project does this run belong
`runName`	Which run was this. An identifier for the sequnece run
`markers`	A list of named sequences.
`samples`	A vector of sample names
`fTags`	A vector of named sequence of MIDs used to barcode samples at the 5' end.
`rTags`	A vector of named sequence of MIDs used to barcode samples at the 3' end.
`inputFastaFile`	The name of the file containing sequences. Currently only fasta format is supported. It is up to you to pre-filter the sequences.
`overwrite`	Should files in the current directory be overwritten? c("prompt", "yes", "no")

This important function stores all the information about the analysis run AND populates the working directory with multiple local Blast databases, which are later required by mlgt. Once prepareMlgtRun has been run, mlgt can be run aswell as printBlastResultGraphs and inspectBlastResults.

An object of class mlgtDesign is returned. Also, several BLAST dbs and sets of BLAST results are created in the working directory. These are essential for mlgt to run.

printBlastResultGraphs and inspectBlastResults can only be run AFTER prepareMlgtRun.

mlgt documentation built on May 1, 2019, 8:45 p.m.