Changelog

Source: NEWS.md

MultiEWCE 0.1.9

New features

• New function: get_bg:
  • Creates and caches background made with gprofiler.
• New function: standardise_genes
  • May move this to orthogene package as it’s quite generally useful.
• Allow users to set min number of genes:
  • min_genes arg in gen_results / ewce_para.

Bug fixes

• gen_results / ewce_para
  • bg was incorrectly set to use only genes in gene_data.
  • Now uses get_bg to create background using gprofiler.
• get_valid_gene_lists
  • Throw error when 0 valid gene lists found.
• get_unfinished_list_names
  • Fix example
• Use rworkflows@dev to avoid API limit.

MultiEWCE 0.1.8

New features

• MultiEWCE finally gets a hex sticker!
• gen_results / gen_overlap
  • Check for existing results and import if already there.
  • Name all results “gen_results.rds” or “gen_overlap.rds” to avoid rerunning duplicate analyses on HPC.
• Update rworkflows.yml

Bug fixes

• Fix unit tests and examples to use “hpo_id” instead of “hpo_name”.
• load_hpo_graph:
  • export
  • Regenerate and update “hpo_graph.rds” file.
• Drastically reduce time to run examples.
• ontology_plot
  • Fix function and add test.
• DESCRIPTION
  • Depends: R (>= 2.10) –> Depends: R (>= 4.1), to ensure |> function available.
  • Rewrite Description field to reflect MultiEWCE’s current purpose.

MultiEWCE 0.1.7

New features

• Update to coordinate with HPOExplorer updates.
• New funcs:
  • plot_ont_lvl
  • ttd_check
  • ttd_plot
  • ttd_import

MultiEWCE 0.1.6

New features

• Require HPOExplorer (>= 0.99.10)
• Switch terms:
  • “HPO_ID” –> “hpo_id”
  • “Phenotype” –> “hpo_name”
  • “FREQUENCY” –> “gene_freq”
  • “Onset” –> “onset”
  • “Modifier” –> “modifier”
  • “Aspect” –> “aspect”
  • “Gene” –> “gene_symbol”
  • “DatabaseID” –> “disease_id”
  • “LinkID” –> “disease_id”
• Update all “data” objects.
• get_data
  • Add tag arg.

Bug fixes

• load_example_results
  • Change tag to “latest”.
  • Update colnames dynamically.
• load_example_ctd
  • Change tag to “latest”.
• load_hpo_graph
  • Change tag to “latest”.
• map_tissues
  • Fix docs.
• agg_results
  • Add “hpo_id” column before aggregation.
• correlation_heatmap
  • Ensure row annot order is correct.
• add_ctd
  • Fix example.

MultiEWCE 0.1.5

New features

• prioritise_targets
  • New arg keep_evidence to utilise GenCC evidence scores provided via HPOExplorer.
  • Merge symptom-level driver genes after unlisting the “intersection” column instead of using indirect approach that on nested “intersection” column.
• prioritise_targets_network
  • Add feature to resize plot after double-click.
• New function: add_tissues
  • Add tissues that each cell type is found in, using a celltype-tissue mapping file.
  • Regenerate “DescartesHuman_celltype_mapping.csv” file as the one previously generated wrong (had every celltype in every tissue)

Bug fixes

• prioritise_targets_network
  • Fill screen better in saved plots with new default args: width = "100%", height = "90vh"

MultiEWCE 0.1.4

New features

• prioritise_targets
  • Move filtering steps and arg docs inside respective HPOExplorer::add_* functions.
• gen_results
  • New arg parallel_boot lets users choose which level to parallelise over.
• New exported func: gen_overlap
  • Compute simple overlap enrichment results.
  • Overcomes requirement of >=4 genes.
  • Faster than EWCE (but less robust)
• New internal func: save_results
• load_example_results
  • New arg force_new

Bug fixes

• get_valid_gene_lists
  • Can now handle any list_name_column

MultiEWCE 0.1.3

New features

• ggnetwork_plot_full:
  • Handles multiple celltypes by aggregation.
• New internal function: agg_results.
• New functions for generating/visualizing prioritised targets:
  • prioritise_targets
  • prioritise_targets_heatmap
  • prioritise_targets_network
  • report_plot
  • correlation_heatmap
  • frequency_bar
  • frequency_histogram
• Added example_targets data:
  • Speeds up run time of examples/tests.

Bug fixes

• Remove unused function: count_results
• Make get_unfinished_list_names much more efficient.
• Add leeway to gen_results test, as the number of sig results varies from run to run.

MultiEWCE 0.1.2

New features

• New functions:
  • load_example_results
  • ontology_plot
  • terminal_celltypes
  • various support functions
• Add ontologyPlot as new Import.
• Was able to replicate Momoko’s results!!!

Bug fixes

• load_example_ctd
  • Pass file to piggyback::pb_download
• Remove redundant get_gene_list function (now handled by HPOExplorer::get_gene_lists).
• Make get_valid_gene_lists much more efficient and consider the intersect between ctd/gene_data genes.
• merge_results:
  • Handle NULL results in list.

MultiEWCE 0.1.1

New features

• Added a NEWS.md file to track changes to the package.
• Added rworkflows
• ewce_para
  • Harmonize arguments with EWCE
  • Set default list_names arg
  • Output named list of saved files instead of TRUE.
  • Add messages that appear in parallel. Make EWCE message silent.
• ewce_plot:
  • Simply make this a shallow wrapper for EWCE::ewce_plot as the latter function has since been fixed.
• Speed up with lapply throughout.
• gen_results:
  • Allow speedup by skipping writing to RDS and returning merged results directly instead.
• Use @inheritParams throughout.
• Use \link throughout.
• load_example_ctd:
  • Cache file
    
• merge_results:
  • Now handles lists of file path AND list of results lists.
• Remove RDA_assign_load
  • Not used and supplanted by EWCE::load_rdata() anyway.
• Remove unnecessary parameter descriptions in MultiEWCE vignette.
• Change results_dir –> save_dir throughout.
• load_example_CTD –> load_example_ctd for function naming consistency.
• Add README.Rmd.

Bug fixes

• Update to use EWCE>1.0.0
• Make more functions internal:
  • is_not_analysed
  • get_valid_gene_lists
• Make paths with file.path instead of hard-coded “/”
• Write files to tempdir() instead of current working directory.
• Remove unused packages:
  • cowplot
  • ewceData
• Fix all unit tests (not set up in correct format originally).