generate_presence_absence {BgeeCall} | R Documentation

## Generate presence absence

### Description

Generate presence absence calls. It correponds to the last part of the generation of the expression calls workflow. It runs the last part of the workflow generating presetn/absent expression calls. This function should only be used by advanced user who already manually run all previous parts of the pipeline. If you are not an advanced user it is safer to run the function “generate_calls_workflow“ that run all steps of the worklow

### Usage

    generate_presence_absence(
      myAbundanceMetadata = new("KallistoMetadata"),
      myBgeeMetadata = new("BgeeMetadata"),
      myUserMetadata
    )

### Arguments

`myAbundanceMetadata` | A descendant object of the Class myAbundanceMetadata (optional).
`myBgeeMetadata` | A Class BgeeMetadata object (optional).
`myUserMetadata` | A Class UserMetadata object.

### Value

path to the 4 output files

### Author(s)

Julien Wollbrett

Julien Roux

### See Also

generate_calls_workflow

### Examples

    {
    # this example reuse data present in the directory 'extdata' of the package.
    user <- new('UserMetadata', working_path = system.file('extdata',
    package = 'BgeeCall'), species_id = '6239', rnaseq_lib_path = system.file(
    'extdata', 'SRX099901_subset', package = 'BgeeCall'),
    annotation_name = 'WBcel235_84', simple_arborescence = TRUE)
    calls_output <- generate_presence_absence(myUserMetadata = user)

    #
    }

[Package BgeeCall version 1.3.1 Index]