loadAnnotation: Load a metaseqR2 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 loads an annotation element from the local annotation database to be used with metaseqr2. If the annotation is not found and the organism is supported, the annotation is created on the fly but not imported in the local database. Use buildAnnotationDatabase for this purpose.

Usage

    loadAnnotation(genome, refdb, 
        level = c("gene", "transcript", "exon"),
        type = c("gene", "exon", "utr"), version="auto",
        db = file.path(system.file(package = "metaseqR2"),
            "annotation.sqlite"), summarized = FALSE, 
            asdf = FALSE, rc = NULL)

Arguments

genome	a metaseqr2 supported organisms or a custom, imported by the user, name. See also the main metaseqr2 man page.
refdb	a metaseqr2 supported annotation source or a custom, imported by the user, name. See also the main metaseqr2 man page.
level	same as the transLevel in metaseqr2.
type	same as the countType in metaseqr2.
version	same as the version in metaseqr2.
db	same as the db in buildAnnotationDatabase.
summarized	if TRUE, retrieve summarized, non-overlaping elements where appropriate (e.g. exons).
asdf	return the result as a data.frame (default FALSE).
rc	same as the rc in buildAnnotationDatabase.

Value

The function returns a GenomicRanges object with the requested annotation.

Author(s)

Panagiotis Moulos

Examples

db <- file.path(system.file(package="metaseqR2"),
    "annotation.sqlite")
if (file.exists(db))
    gr <- loadAnnotation(genome="hg19",refdb="ensembl",
        level="gene",type="gene",db=db)

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