loadAnnotation {metaseqR2} | R Documentation

## Load a metaseqR2 annotation element

### 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)

[Package metaseqR2 version 1.2.0 Index]