| Version: | 0.1.5 |
| Date: | 2018-06-07 |
| Title: | 'tigreBrowser' Database Writer |
| Depends: | R (≥ 2.14.0) |
| Imports: | DBI, RSQLite |
| Description: | Write modelling results into a database for 'tigreBrowser', a web-based tool for browsing figures and summary data of independent model fits, such as Gaussian process models fitted for each gene or other genomic element. The browser is available at https://github.com/PROBIC/tigreBrowser. |
| License: | AGPL-3 |
| URL: | https://github.com/PROBIC/tigreBrowserWriter |
| BugReports: | https://github.com/PROBIC/tigreBrowserWriter/issues |
| RoxygenNote: | 5.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2018-06-07 20:06:30 UTC; ahonkela |
| Author: | Antti Honkela [aut, cre], Miika-Petteri Matikainen [aut] |
| Maintainer: | Antti Honkela <antti.honkela@helsinki.fi> |
| Repository: | CRAN |
| Date/Publication: | 2018-06-07 21:07:56 UTC |
Finalise and close the database
Description
Finalise and close the database
Usage
closeDb(db, experimentSet = "")
Arguments
db |
Database object created by |
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 |
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 |
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 |
experimentName |
Experiment name |
regulatorName |
Regulator name (more detailed experiment identifier) |
filename |
URL path to figures. The path can contain the
special form |
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 |
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 |
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 |
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)