NEWS.md

In richelbilderbeek/gcaer: Interface to GCAE

News

Newest versions at top.

gcaer v0.6.6 (unreleased)

NEW FEATURES

• Added 'check_pheno_model_filename'
• Can run 'do_gcae_experiment' without a 'superpops'
• Added 'get_gcae_model_ids'
• Added 'get_gcae_pheno_model_ids'
• Added 'get_gcae_pheno_model_filenames'
• Added 'read_pheno_model_file'

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

gcaer v0.6.5 (2022-04-08)

NEW FEATURES

• Add 'check_gcae_experiment_params_filename'
• Add 'create_plots_from_gcae_experiment_results'
• Add 'create_test_gcae_experiment_params'
• Add 'read_gcae_experiment_params_file'
• Add 'save_gcae_experiment_params'
• Add 'save_gcae_experiment_results'

MINOR IMPROVEMENTS

• 'check_superpops' also checks for spaces in the filename

BUG FIXES

• None

gcaer v0.6.4 (2022-03-30)

NEW FEATURES

• Add 'analyse_qt_prediction'
• Add 'analyse_qt_prediction_depersonalized'
• Add 'check_epoch'
• Add 'check_metric'
• Add 'check_metrics'
• Add 'create_gcae_evaluate_args'
• Add 'do_gcae_experiment'
• Add 'gcae_evaluate'
• Add 'gcae_train_more'
• Add 'read_gcae_options_file'
• Add 'read_gcae_setup_file'
• Add 'rename_files'
• Add 'save_gcae_options'
• Add 'save_gcae_setup'

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

gcaer v0.6.3 (2022-03-08)

NEW FEATURES

• Add 'check_gcae_experiment_params'
• Add 'check_gcae_input_files'
• Add 'create_gcae_input_data'
• Add 'create_gcae_experiment_params'
• Add 'create_test_gcae_input_data'
• Add 'create_test_gcae_input_filenames'
• Add 'get_test_labels_table'
• Add 'resize_to_shared_individuals_from_data'
• Add 'resize_to_shared_individuals_from_files'
• Add 'save_gcae_input_data'
• Add 'summarise_gcae_input_data'
• Add 'summarise_gcae_input_files'

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Use 'save_labels_table' instead of 'save_labels_file', as the function saves a 'label_table'

gcaer v0.6.1 (2022-02-22)

NEW FEATURES

• Fix GenoCAE's Pheno branch to work well with gcaer
• Add check_gcae_input_data to check that the data can be read by GenoCAE and to give a clear error when it cannot
• Added read_labels_file and save_labels_table to work with a GenoCAE labels file

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

gcaer v0.6 (2022-01-26)

NEW FEATURES

• gcae_folder must be the path to GenoCAE

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

gcaer v0.5.1 (2022-01-25)

NEW FEATURES

• Can specify a separate GenoCAE and ormr folder

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

gcaer v0.5 (2022-01-14)

NEW FEATURES

• Can run GenoCAE from R and do the core of the workflow

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

gcaer v0.4 (2021-12-03)

NEW FEATURES

• Singularity container is based on the ormr Singularity container (which is subsequently based upon the plinkr Singularity container)
• Fixes bug in GenoCAE, use the richelbilderbeek Fork of GCAE as the main repo
• Can run gcae_train on a phenotype

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

gcaer v0.3 (2021-07-30)

NEW FEATURES

• Added Singularity container

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

gcaer v0.2 (2021-07-09)

NEW FEATURES

• Can project GCAE using gcae_project
• Can plot the results of the GCAE using gcae_plot

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

gcaer v0.1 (2021-07-01)

NEW FEATURES

• Can install and uninstall GCAE
• Can run GCAE using run_gcae
• Can train GCAE using gcae_train

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

richelbilderbeek/gcaer documentation built on March 25, 2024, 3:08 p.m.