importCustomAnnotation: Import a metaseqR2 custom annotation element

In metaseqR2: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

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"
#)

metaseqR2 documentation built on Nov. 8, 2020, 7:34 p.m.