importCustomAnnotation {metaseqR2} | R Documentation

## Import a metaseqR2 custom annotation element

### Description

This function creates a local annotation database to be used with metaseqr2 so as to avoid long time on the fly annotation downloads and formatting.

### Usage

        importCustomAnnotation(gtfFile, metadata,
            level = c("gene", "transcript", "exon"),
            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.
`level` | same as the `transLevel` in `metaseqr2`.
`type` | same as the `countType` in `metaseqr2`.

### 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="metaseqR2"),"dummy.gtf"),
        metadata=list(
            organism="dummy",
            source="dummy_db",
            version=1,
            chromInfo=chromInfo
        ),
        level="gene",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"
    #  ),
    #  level="gene",type="gene"
    #)

[Package metaseqR2 version 1.2.0 Index]