R: Prepare to run mlgt

prepareMlgtRun {mlgt} | R Documentation

## 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")

### 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`.

### 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.

### See Also

`printBlastResultGraphs` and `inspectBlastResults` can only be run AFTER `prepareMlgtRun`.

[Package mlgt version 0.16 Index]