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NEWS.md

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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