buildCustomAnnotation {metaseqR2} | R Documentation

## Import custom annotation to the metaseqR2 annotation database from GTF file

### Description

This function imports a GTF file with some custom annotation to the metaseqR2 annotation database.

### Usage

        buildCustomAnnotation(gtfFile, metadata,
        db = file.path(system.file(package = "metaseqR2"),
            "annotation.sqlite"), rewrite=TRUE)

### Arguments

`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 = "metaseqR2"),` `"annotation.sqlite")` that is, the installation path of metaseqR2 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.

### Details

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.

### Value

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

### Author(s)

Panagiotis Moulos

### Examples

    # 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)
    if (.Platform$OS.type == "unix") {
      buildCustomAnnotation(
        gtfFile=file.path(system.file(package="metaseqR2"),"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",
        level="gene",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

[Package metaseqR2 version 1.0.11 Index]