setTranscriptomeFromFile: Set transcriptome_object of one UserMetadata object

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

Set transcriptome_object of one UserMetadata object

Description

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

Usage

setTranscriptomeFromFile(userObject, transcriptomePath, transcriptomeName)

## S4 method for signature 'UserMetadata,character,missing'
setTranscriptomeFromFile(userObject, transcriptomePath, transcriptomeName)

## S4 method for signature 'UserMetadata,character,character'
setTranscriptomeFromFile(userObject, transcriptomePath, transcriptomeName)

Arguments

userObject	The UserMetadata object
transcriptomePath	Absolute path to the transcriptome file
transcriptomeName	(optional) Name of the trancriptome. Will be used to create folders.

Details

If no transcriptomeName is provided the name of the transcriptome file will be used to create folders.

Value

An object of the class UserMetadata

Examples

{
transcriptome_path <- system.file("extdata", "transcriptome.fa", package = "BgeeCall")
user <- new("UserMetadata")
user <- setTranscriptomeFromFile(user, transcriptome_path,
                                 "transcriptome_name")
}

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