buildCustomAnnotation: Import custom annotation to the recoup annotation database...
In recoup: An R package for the creation of complex genomic profile plots

Description Usage Arguments Details Value Author(s) Examples

This function imports a GTF file with some custom annotation to the recoup annotation database.

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    buildCustomAnnotation(gtfFile, metadata,
    db = file.path(system.file(package = "recoup"),
        "annotation.sqlite"), rewrite=TRUE)

`gtfFile`	a GTF file containing the gene structure of the organism to be imported.
`metadata`	a list with additional information about the annotation to be imported. See Details.
`db`	a valid path (accessible at least by the current user) where the annotation database will be set up. It defaults to `system.file(package = "recoup"),` `"annotation.sqlite")` that is, the installation path of recoup package. See also Details.
`rewrite`	if custom annotation found, rwrite? (default `FALSE`). Set to `TRUE` if you wish to update the annotation database for a particular custom annotation.

Regarding the metadata argument, it is a list with specific format which instructs buildCustomAnnotation on importing the custom annotation. Such a list may has the following members:

organism a name of the organism which is imported (e.g. "my_mm9"). This is the only mandatory member.
source a name of the source for this custom annotation (e.g. "my_mouse_db"). If not given or NULL, the word "inhouse" is used.
version a string denoting the version. If not given or NULL, current date is used.
chromInfo it can be one of the following:
- a tab-delimited file with two columns, the first being the chromosome/sequence names and the second being the chromosome/sequence lengths.
- a BAM file to read the header from and obtain the required information
- a data.frame with one column with chromosome lengths and chromosome names as rownames.

See the examples below for a metadata example.

Regarding db, this controls the location of the installation database. If the default is used, then there is no need to provide the local database path to any function that uses the database (e.g. the main metaseqr2). Otherwise, the user will either have to provide this each time, or the annotation will have to be downloaded and used on-the-fly.

The function does not return anything. Only the SQLite database is created or updated.

Panagiotis Moulos

# Dummy database as example
customDir <- file.path(tempdir(),"test_custom")
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)
buildCustomAnnotation(
  gtfFile=file.path(system.file(package="recoup"),"dummy.gtf"),
  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

## Real data!
## Setup a temporary directory to download files etc.
#customDir <- file.path(tempdir(),"test_custom")
#dir.create(customDir)

#myDb <- file.path(customDir,"testann.sqlite")

## Gene annotation dump from Ensembl
#download.file(paste0("ftp://ftp.ensembl.org/pub/release-98/gtf/",
#  "dasypus_novemcinctus/Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz"),
#  file.path(customDir,"Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz"))

## Chromosome information will be provided from the following BAM file
## available from Ensembl
#bamForInfo <- paste0("ftp://ftp.ensembl.org/pub/release-98/bamcov/",
#  "dasypus_novemcinctus/genebuild/Dasnov3.broad.Ascending_Colon_5.1.bam")

## Build with the metadata list filled (you can also provide a version)
#buildCustomAnnotation(
#  gtfFile=file.path(customDir,"Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz"),
#  metadata=list(
#    organism="dasNov3_test",
#    source="ensembl_test",
#    chromInfo=bamForInfo
#  ),
#  db=myDb
#)

## Try to retrieve some data
#dasGenes <- loadAnnotation(genome="dasNov3_test",refdb="ensembl_test",
#  level="gene",type="gene",db=myDb)
#dasGenes