generate_presence_absence: Generate presence absence
In BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation

Description Usage Arguments Value Author(s) See Also Examples

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

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

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

path to the 4 output files

Julien Wollbrett

Julien Roux

generate_calls_workflow

{
# 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)

#
}