setAnnotationFromFile: Set annotation_object of one UserMetadata object

In BgeeDB/BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation

Set annotation_object of one UserMetadata object

Description

Method of the class UserMetadata. Set annotation_object of one UserMetadata object by providing the path to a fasta transcriptome file.

Usage

setAnnotationFromFile(userObject, annotationPath, annotationName)

## S4 method for signature 'UserMetadata,character,missing'
setAnnotationFromFile(userObject, annotationPath, annotationName)

## S4 method for signature 'UserMetadata,character,character'
setAnnotationFromFile(userObject, annotationPath, annotationName)

Arguments

userObject	The UserMetadata object
annotationPath	Absolute path to the annotation file
annotationName	(optional) Name of the annotation. Will be used to create folders.

Details

If no annotationName is provided the name of the annotation file will be used to create folders.

Value

An object of the class UserMetadata

Examples

{
# path to gtf annotation file
annotation_file <- system.file("extdata", "annotation.gtf", package = "BgeeCall")
user <- new("UserMetadata")
user <- setAnnotationFromFile(user, annotation_file,
                             "annotation_name")
}

BgeeDB/BgeeCall documentation built on Nov. 10, 2023, 5:40 a.m.