loadAnnotation: Load a recoup annotation element

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

Load a recoup annotation element

Description

This function creates loads an annotation element from the local annotation database to be used with recoup. 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, 
        type = c("gene", "exon", "utr"), version="auto",
        db = file.path(system.file(package = "recoup"),
            "annotation.sqlite"), summarized = FALSE, 
            asdf = FALSE, rc = NULL)

Arguments

genome	a recoup supported organisms or a custom, imported by the user, name. See also the main recoup man page.
refdb	a recoup supported annotation source or a custom, imported by the user, name. See also the main recoup man page.
type	one of the "gene", "exon" or "utr".
version	same as the version in recoup.
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="recoup"),
  "annotation.sqlite")
if (file.exists(db))
  gr <- loadAnnotation(genome="hg19",refdb="ensembl",
    type="gene",db=db)

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