Package 'tigreBrowserWriter'

Finalise and close the database

Description

Finalise and close the database

Usage

closeDb(db, experimentSet = "")

Arguments

db	Database object created by initializeDb
experimentSet	Name of the experiment set for all the experiments (optional)

Examples

db <- initializeDb("", "My Dataset")
  # ...
  closeDb(db)

---

Create and initialize a database

Description

Create and initialize a database

Usage

initializeDb(dbPath, datasetName, datasetSpecies = "", datasetSource = "",
  datasetPlatform = "", datasetDescription = "", datasetSaveLocation = "",
  datasetFigureFilename = "")

Arguments

dbPath	Path to the database file to be created. Empty string
datasetName	Name of the data set
datasetSpecies	Optional data set metadata: species
datasetSource	Optional data set metadata: source
datasetPlatform	Optional data set metadata: platform
datasetDescription	Optional data set metadata: description
datasetSaveLocation	Optional data set metadata: save location
datasetFigureFilename	Optional data set metadata: figure file name

Value

A database object db needed by other tigreBrowserWriter functions

Examples

## Not run: 
  # Create a real database to a file
  db <- initializeDb("/path/to/the/database.sqlite", "My Dataset")
  closeDb(db)

## End(Not run)

  # Create a temporary database to be deleted at the end
  db <- initializeDb("", "My Dataset")
  closeDb(db)

---

Insert aliases

Description

Insert aliases

Usage

insertAliases(db, aliasType, aliases, aliasSource = "",
  aliasDescription = "")

Arguments

db	Database object created by initializeDb
aliasType	Name of the alias
aliases	A vector of aliases with names giving the primary identifiers
aliasSource	Optional alias metadata: source
aliasDescription	Optional alias metadata: description

Value

An updated database object db

Examples

db <- initializeDb("", "My Dataset")
  aliases <- c("aliasA", "aliasB", "aliasC")
  names(aliases) <- c("A", "B", "C")
  db <- insertAliases(db, "testalias", aliases)
  closeDb(db)

---

Insert figure data directly to the database

Description

Insert figure data directly to the database

Usage

insertFigureData(db, experimentName, regulatorName, filenames, name = "",
  description = "", priority = 0)

Arguments

db	Database object created by initializeDb
experimentName	Experiment name
regulatorName	Regulator name (more detailed experiment identifier)
filenames	A list of file names of PNG figures. names of the list must correspond to the names of the entities the figures are for.
name	Optional figure name
description	Optional figure description
priority	Integer priority used for sorting figures (default: 0)

Value

An updated database object db

Examples

db <- initializeDb("", "My Dataset")
  logl <- c(-4.0, -2.0, 0.0)
  names(logl) <- c("A", "B", "C")
  baselogl <- c(1.0, -1.0, 4.0)
  names(baselogl) <- names(logl)
  db <- insertResults(db, "testexperiment", "testregulator", "",
                      logl, baselineloglikelihoods=baselogl)
  # Generate a dummy plot (reused for all data elements for simplicity)
  examplefile <- tempfile("plot", fileext=".png")
  png(examplefile)
  plot(c(0, 1), c(0, 1))
  dev.off()
  figures <- list(A=examplefile, B=examplefile, C=examplefile)
  db <- insertFigureData(db, "testexperiment", "testregulator",
                         figures)
  closeDb(db)

---

Insert figure links

Description

Insert figure links

Usage

insertFigures(db, experimentName, regulatorName, filename, name = "",
  description = "", priority = 0)

Arguments

db	Database object created by initializeDb
experimentName	Experiment name
regulatorName	Regulator name (more detailed experiment identifier)
filename	URL path to figures. The path can contain the special form ${probe_name} which will be substituted by the name of the entity (gene, ...) by the browser.
name	Optional figure name
description	Optional figure description
priority	Integer priority used for sorting figures (default: 0)

Value

An updated database object db

Examples

db <- initializeDb("", "My Dataset")
  logl <- c(-4.0, -2.0, 0.0)
  names(logl) <- c("A", "B", "C")
  baselogl <- c(1.0, -1.0, 4.0)
  names(baselogl) <- names(logl)
  db <- insertResults(db, "testexperiment", "testregulator", "",
                     logl, baselineloglikelihoods=baselogl)
  db <- insertFigures(db, "testexperiment", "testregulator",
                      "http://foo.invalid/path/${probe_name}_fit.png")
  closeDb(db)

---

Insert results

Description

Insert results

Usage

insertResults(db, experimentName, regulatorName, figurePath, loglikelihoods,
  baselineloglikelihoods = NA, experimentDesc = "", loopVariable = 2,
  modelTranslation = FALSE, numberOfParameters = NA, parameterNames = NA,
  experimentProducer = "", experimentTimestamp = "", parameters = NA)

Arguments

db	Database object created by initializeDb
experimentName	Experiment name
regulatorName	Regulator name (more detailed experiment identifier)
figurePath	URL path to figures
loglikelihoods	A vector of log-likelihoods of elements identified by names
baselineloglikelihoods	A vector of baseline log-likelihoods of elements identified by names (optional)
experimentDesc	Optional experiment description
loopVariable	Optional: Loop variable (1=regulator, 2=target (default))
modelTranslation	Optional: For gene regulation models, is translation modelled
numberOfParameters	Optional: Number of parameters
parameterNames	Optional: Parameter names
experimentProducer	Optional: Experiment producer (string)
experimentTimestamp	Optional: Experiment timestamp (string)
parameters	Optional: A vector of parameter values for the model

Value

An updated database object db

Examples

db <- initializeDb("", "My Dataset")
  logl <- c(-4.0, -2.0, 0.0)
  names(logl) <- c("A", "B", "C")
  baselogl <- c(1.0, -1.0, 4.0)
  names(baselogl) <- names(logl)
  db <- insertResults(db, "testexperiment", "testregulator", "",
                     logl, baselineloglikelihoods=baselogl)
  closeDb(db)

---

Insert supplementary data

Description

Insert supplementary data

Usage

insertSupplementaryData(db, name, suppData, regulatorName = NA, source = "",
  platform = "", description = "")

Arguments

db	Database object created by initializeDb
name	Name of the supplementary data
suppData	A vector of supplementary data of elements identified by names
regulatorName	Regulator name the data links to (optional)
source	Optional annotation: source
platform	Optional annotation: platform
description	Optional annotation: description

Value

An updated database object db

Examples

db <- initializeDb("", "My Dataset")
  suppdata <- c(1, 2, 3)
  names(suppdata) <- c("A", "B", "C")
  db <- insertSupplementaryData(db, "supptest", suppdata)
  boolsupp <- c(TRUE, TRUE, FALSE)
  names(boolsupp) <- names(suppdata)
  db <- insertSupplementaryData(db, "supptest_bool", boolsupp)
  closeDb(db)

---

Insert data z-scores used for filtering

Description

Insert data z-scores used for filtering

Usage

insertZScores(db, zscores)

Arguments

db	Database object created by initializeDb
zscores	A vector of z-scores of elements identified by names

Value

An updated database object db

Examples

db <- initializeDb("", "My Dataset")
  zscores <- c(1, 2, 3)
  names(zscores) <- c("A", "B", "C")
  db <- insertZScores(db, zscores)
  closeDb(db)

---