NEWS.md

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

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
  • Add new ctd_allAIBS: https://github.com/neurogenomics/MAGMA_Celltyping/issues
• 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: https://github.com/neurogenomics/MAGMA_Celltyping/pull/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: https://github.com/neurogenomics/MAGMA_Celltyping/pull/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

• Fix GHA pkgdown building:
  • The newest version of git introduced bugs when building pkgdown sites from within Docker containers (e.g. via my Linux GHA workflow). Adjusting GHA to fix this.

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 ``

NathanSkene/MAGMA_Celltyping documentation built on May 19, 2024, 7:23 a.m.