importCustomAnnotation {recoup} | R Documentation

## Import a recoup custom annotation element

### Description

This function imports GenomicRanges to be used with recoup from a local GTF file.

### Usage

        importCustomAnnotation(gtfFile, metadata,
            type = c("gene", "exon", "utr"))

### 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. The same as in the `buildCustomAnnotation` man page.
`type` | one of the `"gene"`, `"exon"` or `"utr"`.

### Value

The function returns a `GenomicRanges` object with the requested annotation.

### Author(s)

Panagiotis Moulos

### Examples

    # Dummy GTF as example
    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)
    myGenes <- importCustomAnnotation(
      gtfFile=file.path(system.file(package="recoup"),"dummy.gtf"),
      metadata=list(
        organism="dummy",
        source="dummy_db",
        version=1,
        chromInfo=chromInfo
      ),
      type="gene"
    )

    ## Real data!
    ## 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(tempdir(),"Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz"))

    ## Build with the metadata list filled (you can also provide a version)
    #dasGenes <- importCustomAnnotation(
    #  gtfFile=file.path(tempdir(),"Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz"),
    #  metadata=list(
    #    organism="dasNov3_test",
    #    source="ensembl_test"
    #  ),
    #  type="gene"
    #)

[Package recoup version 1.20.1 Index]