removeAnnotation: Remove an annotation from a sitadela database

In pmoulos/sitadela: An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

Remove an annotation from a sitadela database

Description

This function removes a specific annotation from a sitadela database. It does not support multiple organism, resource and version removal for now.

Usage

    removeAnnotation(org, refdb, ver = NULL, db = NULL)

Arguments

org	an existing organism to remove from the database. See also addAnnotation and addCustomAnnotation for details.
refdb	an existing annotation source to remove from the database. See also addAnnotation and addCustomAnnotation for details.
ver	an existing annotation version to remove from the database. See also addAnnotation and addCustomAnnotation for details. If NULL (default), all versions corresponding to org and refdb will be removed.
db	the database to remove from, defaults to getDbPath().

Value

The function return the number of rows removed from the database contents table.

Author(s)

Panagiotis Moulos

Examples

# Dummy database as example
customDir <- file.path(tempdir(),"test_remove")
dir.create(customDir)

myDb <- file.path(customDir,"testann.sqlite")
chromInfo <- data.frame(length=c(1000L,2000L,1500L),
    row.names=c("A","B","C"))

# Build with the metadata list filled (you can also provide a version)
if (.Platform$OS.type == "unix") {
    addCustomAnnotation(
        gtfFile=file.path(system.file(package="sitadela"),
            "dummy.gtf.gz"),
        metadata=list(
            organism="dummy",
            source="dummy_db",
            version=1,
            chromInfo=chromInfo
        ),
        db=myDb
    )

    # Try to retrieve some data
    myGenes <- loadAnnotation(genome="dummy",refdb="dummy_db",
        type="gene",db=myDb)
    myGenes
    
    # Now remove
    n <- removeAnnotation("dummy","dummy_db",1,myDb)
}

pmoulos/sitadela documentation built on May 19, 2024, 3:52 a.m.