importCustomAnnotation: Import a metaseqR2 custom annotation element

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

Import a metaseqR2 custom annotation element

Description

This function imports a custom GTF/GFF file in a manner helpful for the addition of custom annotations to sitadela.

Usage

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

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 addCustomAnnotation man page.
type	same as the type in loadAnnotation.

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)
if (.Platform$OS.type == "unix" && !grepl("^darwin",R.version$os)) {
    myGenes <- importCustomAnnotation(
        gtfFile=file.path(system.file(package="sitadela"),
            "dummy.gtf.gz"),
        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"
#)

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