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MAGMA.Celltyping 2.0.14

New features

  • Make sure get_example_gwas caches data.

Bug fixes

  • create_gene_covar_file: Add check to drop duplicate cell types (after ignoring case)
  • load_magma_results_file: Update message to include scenario where cell types dropped due to be duplicated.

MAGMA.Celltyping 2.0.13

New features

Bug fixes

  • Update URLs for getting MAGMA reference genome files (#154).
  • test-magma_links.R: package_version comparisons now only work with strings instead of numbers.

MAGMA.Celltyping 2.0.12

Bug fixes

  • Update URLs for getting MAGMA executables.

MAGMA.Celltyping 2.0.11

New features

  • map_snps_to_genes:
    • expose storage_dir arg to check_genomeLocFile.

Bug fixes

  • create_fake_gwas_path
    • Don't remove "MAGMA_Files" from all parts of path.
  • magma_files_metadata
    • Update metadata.

Bug fixes

  • Fix GHA downloads with "libcurl" settings.

MAGMA.Celltyping 2.0.10

New features

  • map_snps_to_genes
    • Add new duplicate arg to control what to do with duplicate/non-bilalleic SNPs.
    • Add new synonym_dup arg to control what to do with synonymous SNPs.
    • Add subfunctions check_duplicate, check_synonym_dup
  • Add bug/feature report note to startup message.

Bug fixes

  • get_magma_paths
    • Uses file.path instead of hard-coded "/" symbols.
  • map_snps_to_genes -->
    • decompress wasn't recognizing files with ".bgz" suffix.

MAGMA.Celltyping 2.0.9

New features

  • Update tags from "latest" to "v2.0.0" and "v2.0.8"
    • Did this so I can better version-control each Release. Plus I'm renaming some CTDs to make them more intuitive.
    • Also adding some new CTDS: "TabulaMuris_droplet", "TabulaMuris_facs"
  • get_data / get_ctd
    • Expose .token arg.
    • Expose tag arg.
    • Make token error instructions more explicit and add GH docs link.

MAGMA.Celltyping 2.0.8

New features

  • Add rworkflows
    • GHA
    • Replace badger
  • get_ctd_dendro
    • Automatically compute spec quantiles matrix when its missing.
  • plot_celltype_associations
    • Replace sprintf, for,
    • Control verbosity
    • Replace grid with patchwork
    • Save with ggplot2::ggsave instead of grDevices
    • Reduce redundancy in code (e.g. saving plots)
    • Add new arg to bind plots from multiple levels into one: bind_plots
  • enrichment_results
    • Update example enrichment results to new format with nested levels.
  • Add CITATION file.
  • Add citation info and volcano/cell icons to startup message.
  • Replace %>% with |> syntax.
  • celltype_associations_pipeline:
    • Print error messages.
  • get_ctd
  • map_snps_to_genes
    • Fix genesOut path for Windows.
    • Subfunctionalize :check_n, check_genomeLocFile
  • enrichment_results:
    • Update example results with extra slots and named levels.
  • Added raw MAGMA results file as an example:
    • "inst/extdata/ieu-a-298.tsv.gz.35UP.10DOWN.level1.MainRun.gsa.out"
  • calculate_conditional_celltype_associations
    • Pass up new arg: qvalue_thresh
    • Add unit tests that test for non-NULL results.
    • Ensure the BASELINE
  • test-celltype_associations_pipeline.r
    • Add unit tests for additional CTDs (e.g. "ctd_AIBS","ctd_Aerts2018").
  • magma_tileplot
    • Replace grDevices / gridExtra with patchwork
    • Move legend to top
    • Add axis labels
    • Add unit tests
  • Add new function fix_celltype_names2 for situations when you don't want to make all celltypes in vector unique.
  • Add unit tests for interactive check_n func

Bug fixes

  • plot_celltype_associations
    • Fix issues described in PR: #121
    • Fix NAs issue by ensuring celltype names in ctAssocs and ctdDendro are both run through EWCE::fix_celltype_names() when creating an ordered factor.
  • merge_magma_results
    • Add names to levels
  • calculate_celltype_associations:
    • Fix issue raised here: #135
    • Made flags conditional on MAGMA version.
    • Subfunctionalize: calculate_celltype_associations_linear, calculate_celltype_associations_top10
    • Ensure EnrichmentMode gets added to the saved file names to distinguish results from one another via new internal func: check_analysis_name.
  • load_magma_results_file
    • Was incorrectly giving >50% of celltypes missing. %s celltypes error whenever Top10% + conditional was being used.
    • Remove creations of res$COVAR column, as this is no longer relevant given the structure of the results table.
    • Remove outdated steps to fix celltype names, which were very roundabout and convoluted.
    • Don't set rownames(res) <- res$VARIABLE as this causes duplicate rownames.
    • Now exported
    • Add new column "analysis_name"
    • Add new arg: keep_types= to subset results types.
  • map_snps_to_genes
    • Fix bug preventing automatic detection of "N" column.

MAGMA.Celltyping 2.0.7

New features

  • plot_celltype_associations: added unit tests.
  • calculate_conditional_celltype_associations: added unit tests.
    • Also runs calculate_celltype_associations internally.

Bug fixes

  • Get GitHub Actions to pass on all 3 OS.

MAGMA.Celltyping 2.0.6

New features

  • import_magma_files:
    • Add args to import as nested list and/or data.tables.
    • Add dedicated unit tests.
  • magma_files_metadata
    • Update after deleting old files.
  • celltype_associations_pipeline:
    • Pass up standardise arg.
  • adjust_zstat_in_genesOut:
    • Enable usage without CTD.
    • Add unit tests.
  • Infer ctd and geneset species by default:
    • infer_ctd_species
    • infer_geneset_species
  • map_snps_to_genes:
    • Can interpret N when =NULL or =NA.
    • Added genes_only arg to make function faster and skip generating "genes.raw" file.

Bug fixes

  • Ensure all functions work with sparse matrices.
  • check_quantiles:
    • Compute "specificity_quantiles" if not already present in CTD (workaround for bug in EWCE::standardise_ctd).
  • decompress
    • Specify file path as storage_dir instead of tempdir().
  • Update full_workflow vignette to work.
  • magma_tileplot:
    • Fix to handle situations where all q-values equal 1.
  • get_example_gwas:
    • Revert default storage dir to tempdir() to make easier to infer MAGMA output file paths in vignettes.
  • merge_results:
    • Createsave_dir if not already present.
  • get_driver_genes:
    • Fix bug that searched for "hgnc.symbol" instead of "hgnc_symbol".
    • Sort by mean rank between "ADJ_ZSTAT" and "specificity_proportion".
  • magma_files_metadata:
    • Updated to reflect newly reprocessed 288 datasets.
    • Reprocessed "ukb-b-6548" to get calculate_conditional_celltype_enrichment_limma example working again.

MAGMA.Celltyping 2.0.5

New features

  • get_ctd:
    • Documented new CTDs from model celltype conservation project.
    • Added better documentation for each of the other CTDs as well (including references).
    • Re-standardized all CTD with updated EWCE::standardise_ctd function.
    • Enabled download of multiple CTDs in one call.
    • Cached all CTDs (not in tempdir).
    • Import either RDS or RDA files.

MAGMA.Celltyping 2.0.4

Bug fixes

MAGMA.Celltyping 2.0.3

Bug fixes

  • Ensure get_genome_ref saves to cache dir (not temp dir) during map_snps_to_genes.
  • Fix GHA release/devel conflicts.
  • Add optional error handling with GitHub PAT fix instructions to get_data, specifically get_genomeLocFile.
  • Construct URLs with paste instead of file.path to avoid cross-platforms issues (e.g. Windows inserting "" instead of "/").
  • Add dir.create to get_data.

MAGMA.Celltyping 2.0.2

New features

  • get_genomeLocFile: Store NCBI ref file in cache dir by default.

Bug fixes

  • Add windows-specific files/folders to .Rbuildignore.
  • Bump Depends to R(>= 4.1).

MAGMA.Celltyping 2.0.1

New features

  • get_example_gwas_raw: Allow users to specify timeout when downloading raw (pre-munged) files.
  • Added Docker/Singularity vignette, with link in README.
  • Add --as-cran to R CMD check in GHA.

Bug fixes

  • Add $annot data.frames to each ctd in get_ctd to make compatible with all EWCE functions.
  • Add "ctd_DescartesHuman" to documented datasets in get_ctd.

MAGMA.Celltyping 2.0.0

  • MAJOR UPGRADE: MAGMA.Celltyping was revamped to meet CRAN standards, automatically install MAGMA, and take any species are input.

New features

  • Added a NEWS.md file to track changes to the package.
  • Automatically install MAGMA with new magma_install function; stores binaries in MAGMA.Celltyping-specific cache dir. Added various support functions to make this possible and ensure correct version is being used.
  • Added magma_uninstall function to remove one or all MAGMA binaries.
  • Allow MAGMA.Celltyping to install even if MAGMA is not installed. Instead, check at the beginning of functions that require MAGMA using magma_check.
    • magma_links_stored: Include built-in metadata with links to all MAGMA versions with parsed version numbers, OS, and which is the latest version.
  • Call MAGMA commands with magma_run which finds the requested version of MAGMA and uses it.
  • Print readable, user-friendly MAGMA commands when being run through magma_cmd function.
  • Added unit tests.
  • Create hex sticker
  • New function: get_sub_SNP_LOC_DATA
  • Formally deprecated functions using .Deprecated function and removing all other internal code:
    • get_genomebuild_for_sumstats
    • build_snp_location_tables
    • format.sumstats.for.magma
    • format_sumstats_for_magma_macOnly
    • standardise.sumstats.column.headers
    • standardise.sumstats.column.headers.crossplatform
  • Removed sumstatsColHeaders from data, as it was only used in now-deprecated functions.
  • Renamed all functions with "." to "_" to meet coding standards.
  • Renamed functions to be more concise and avoid issues with test file names being too long:
    • calculate.celltype.enrichment.probabilities.wtLimma --> calculate_celltype_enrichment_limma
    • calculate.conditional.celltype.enrichment.probabilities.wtLimma --> calculate_conditional_celltype_enrichment_limma
  • Removed all large data/ to GitHub Releases, now accessible with dedicated piggyback-based functions:
    • get_ctd: CellTypeDatasets
    • get_example_gwas: GWAS summary stats
    • get_genomeLocFile: NCBI gene coordinate references.
  • Create example full GWAS summary stats (both unfiltered and filtered + munged with MungeSumstats). Accessed by get_example_gwas.
    • "prospective_memory"
    • "fluid_intelligence"
    • "educational_attainment"
  • Updated vignettes:
    • Created concise Getting started vignette.
    • Updated origiinal vignette and turned into full_workflow vignette.
  • Made certain functions run automatically internally, instead of having the user run them:
    • get_genome_ref
    • prepare_quantile_groups
  • Remove unnecessary dependencies:
    • reshape
    • cowplot
    • SNPlocs.Hsapiens.dbSNP144.GRCh37
    • SNPlocs.Hsapiens.dbSNP144.GRCh38
  • Replaced hgnc2entrez with improved hgnc2entrez_ortohgene from orthogene::all_genes. Benchmarked to confirm that the latter increases the number of genes that can be converted.
  • Allow all functions to accept datasets/gene lists from any species. Now automatically converted to output_species (default: "human") using orthogene.
  • Create MAGMA files repository using various OpenGWAS datasets that have been munged with MungeSumstats: MAGMA_Files_Public
    • magma_files_metadata: Built-in table of all pre-processed MAGMA files currently in the database.
  • Added API to search and access MAGMA files repository: import_magma_files.
  • Allow all relevant functions to take only MAGMA files as input (instead of requiring the GWAS summary stats); e.g. calculate_celltype_associations(magma_dir="<folder_containing_magma_files>") This function is also used for downloading MAGMA files in examples/unit tests.
  • Add header notation in code comments to improve code navigability.
  • Fix Roxygen notes:
    • Document @title,@description,@param, @return for all exported (and many internal) functions.
    • Document @examples for all exported (and many internal) functions.
    • Used @importFrom or requireNamespace for all imports functions.
  • Replace usage of all 1:10 syntax.
  • Reduce number of functions in NAMESPACE
  • Set all defaults consistently across all functions:
    • upstream_kb = 35
    • downstream_kb = 10
  • Allow the use of non-European populations by downloading population-specific LD panels from 1KG with get_genome_ref(population = "<population_name>")
  • Handle other CTD matrix input types by ensuring standardisation as dense matrices when computing quantiles/normalization.
  • Take advantage of new EWCE features in bschilder_dev branch:
    • Standardise CTD internally in all relevant functions using new EWCE::standardise_ctd
  • Create all-in-one functions celltype_associations_pipeline, which lets users specify which test they want to run with arguments, including:
    • calculate_celltype_associations (Linear mode)
    • calculate_celltype_associations (Top10% mode)
    • calculate_conditional_celltype_associations
  • Parallelise celltype_associations_pipeline across multiple cores.
  • Removed old functions whose output were not being used:
    • normalise_mean_exp
    • bin_specificityDistance_into_quantiles
    • bin_expression_into_quantiles
  • Add new function (plus tests):
    • get_driver_genes
  • Added unit tests for:
    • calculate_celltype_enrichment_limma
    • adjust_zstat_in_genesOut
    • Deprecated functions
  • Added R script to produce vignette results inst/extdata/MAGMA_Celltyping_1.0_vignette.R, and uploaded zipped folder via piggyback: MAGMA_Celltyping_1.0_results.zip
  • Added unit tests comparing old (1.0.0) vs new (>=2.0) MAGMA.Celltyping versions produce the same results; test-MAGMA_Celltyping_1.0_vs_2.0.R. Full report here.

Bug fixes

  • Removed usethis call from code.
  • Removed all library calls from code.
  • Avoid accidentally renaming columns with data.frame
  • Remove all suppressWarnings calls and resolve the underlying issues instead.
  • Add utils as Suggest.
  • Normalize paths to magma executables (to avoid path issues on WindowsOS).
  • Fixed axes in plot_celltype_associations, first reported here.
  • Fixed prepare_quantile_groups so that it's consistent with how EWCE compute specificity quantiles. Ensures that all celltypes (columns) have exactly the same number of quantiles, which was not the case before.
  • Fixed bug in ``