export: Export results to an SQLite database

In ahonkela/tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression

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)

ahonkela/tigre documentation built on Aug. 6, 2021, 12:08 p.m.