generate_presence_absence: Generate presence absence

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

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 present/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

Sara Fonseca Costa

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)

#
}

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