importCustomAnnotation: Import a recoup custom annotation element

In pmoulos/recoup: An R package for the creation of complex genomic profile plots

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"
#)

pmoulos/recoup documentation built on May 20, 2024, 2:22 a.m.