mlgt (version 0.16)

prepareMlgtRun: Prepare to run mlgt

Description

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

Usage

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

Arguments

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")

Value

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.

Details

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.

See Also

printBlastResultGraphs and inspectBlastResults can only be run AFTER prepareMlgtRun.