Skip to content

Latest commit

 

History

History
169 lines (148 loc) · 8.01 KB

NEWS.md

File metadata and controls

169 lines (148 loc) · 8.01 KB

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 ``