export.scores {tigre} | R Documentation

## Export results to an SQLite database

### Description

Exports the results to an SQLite database which can then be browsed with a result browser. The function will export log likelihoods, z-scores, model figures and gene aliases.

### Usage

      export.scores(scores, datasetName='', experimentSet='',
        databaseFile='database.sqlite', preprocData=NULL, models=NULL,
        figpath=NULL, aliasTypes=c("SYMBOL", "GENENAME", "ENTREZID"),
        datasetSource='', datasetDescription='',
        datasetSaveLocation='', datasetFigureFilename='',
        experimentTimestamp=as.character(Sys.Date()),
        figureDesc='', figurePrio=0, regulator=NULL)

### Arguments

`scores` | The scoreList to export.
`datasetName` | Name of the dataset in the database.
`experimentSet` | Name of the experiment set in the database.
`databaseFile` | Filename of the database. New database is created if the file does not exist.
`preprocData` | Preprocessed data. This is required in order to generate models and figures and to calculate z-scores. Also, inserting aliases requires preprocessed data.
`models` | Learned models. If not given, the function will generate models if preprocessed data is available.
`figpath` | Figure path. If this is defined, the function will generate figures to the given path instead of inserting them to the database.
`aliasTypes` | Types of aliases that are inserted to the database.
`datasetSource` | Additional information that is inserted to the database if defined.
`datasetDescription` | Additional information that is inserted to the database if defined.
`datasetSaveLocation` | Additional information that is inserted to the database if defined.
`datasetFigureFilename` | Additional information that is inserted to the database if defined.
`experimentTimestamp` | Timestamp that is inserted to the database. The default value is current date in ISO-8601 format.
`figureDesc` | Additional information that is inserted to the database if defined.
`figurePrio` | Additional information that is inserted to the database if defined.
`regulator` | If defined, override the regulator name from scoreList.

### Author(s)

Miika-Petteri Matikainen, Antti Honkela

### See Also

`GPRankTargets, GPRankTFs`.

### Examples

    ## Not run:
      # Load a mmgmos preprocessed fragment of the Drosophila developmental
      # time series
      data(drosophila_gpsim_fragment)

      # FBgn names of target genes
      targets <- c('FBgn0003486', 'FBgn0033188', 'FBgn0035257')
      # Load gene annotations
      library(annotate)
      aliasMapping <- getAnnMap("ALIAS2PROBE",
                      annotation(drosophila_gpsim_fragment))

      # Get the probe identifier for TF 'twi'
      twi <- get('twi', env=aliasMapping)
      # Load alternative gene annotations
      fbgnMapping <- getAnnMap("FLYBASE2PROBE",
                     annotation(drosophila_gpsim_fragment))

      # Get the probe identifiers for target genes
      targetProbes <- mget(targets, env=fbgnMapping)

      # Rank the targets, filtering weakly expressed genes with average
      # expression z-score below 1.8
      scores <- GPRankTargets(drosophila_gpsim_fragment, TF=twi,
                              testTargets=targetProbes,
                              options=list(quiet=TRUE),
                              filterLimit=1.8)

      # Export data from scoreList and preprocessed data to a database
      export.scores(scores, datasetName='Drosophila',
                    experimentSet='GPSIM/GPDISIM',
                    database='database.sqlite',
                    preprocData=drosophila_gpsim_fragment,
                    aliasTypes=c('SYMBOL', 'GENENAME', 'FLYBASE', 'ENTREZID'))

    ## End(Not run)

[Package tigre version 1.34.0 Index]