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locusPackRat 0.7.0

New Features

  • lpr_check() / checkPackRat(): diagnostic function that validates project state, checks file integrity, and reports optional dependency status
  • lpr_* aliases for all 12 exported functions (e.g., lpr_init, lpr_export, lpr_query_ot) — easier tab-completion and discoverability; both CamelCase and lpr_* names work identically
  • New vignette: new_ux_features demonstrating check and alias usage

Improvements

  • Moved plotgardener and httr from Imports to Suggests with requireNamespace() guards, reducing the install footprint for users who don't need locus zoom plots or MouseMine queries
  • buildPacket() zip creation now tries the zip R package first, then falls back to system zip, with an informative error if neither is available
  • Expanded README with install instructions for all 4 genome builds (hg38, hg19, mm39, mm10) and lpr_* quick-start examples

Internal

  • Consolidated duplicate helpers (.render_genes, .standardize_chrom) and %||% operator into single definitions
  • Added zip to Suggests

locusPackRat 0.6.3

Bug Fixes

  • Locus zoom chromosome matching: Added .standardize_chrom() helper that normalizes chromosome columns in scan and signal tables before rendering. Strips "chr" prefix from chrom values so they match pgParams convention (derived from regions.csv). Previously, data with "chr3" in chrom would silently produce an empty Manhattan/signal panel because it didn't match "3" from pgParams.
  • Missing .standardize_chrom() function: The function was referenced in generateLocusZoomPlot() but absent from source, causing errors on fresh installs. Now defined in plotZoom.R.

Improvements

  • generateLocusZoomPlot() now checks for GenomicFeatures package availability before attempting gene track rendering, with a clear install message on failure
  • Added GenomicFeatures to Suggests in DESCRIPTION

Notes

  • Users with Seqinfo >= 1.0.0 (Bioconductor 3.21+) should ensure GenomeInfoDb >= 1.46.0 is installed. Older GenomeInfoDb versions conflict with the Seqinfo package split, causing plotGenes() to fail with an opaque seqinfo method dispatch error. Upgrade via: mamba install -c bioconda bioconductor-genomeinfodb=1.46.2 or BiocManager::install("GenomeInfoDb")

locusPackRat 0.6.2

New Features

  • buildPacket(): new exported function that zips the contents of .locusPackRat/output/ into a single shareable archive with an auto-generated README.md summarizing project metadata, supplementary data sources, and included files
  • buildPacket(include_supplementary): optionally bundles raw supplementary CSVs from .locusPackRat/supplementary/ into the zip. Accepts FALSE (default), TRUE (all tables), or a character vector of specific table names. Files are placed in a supplementary/ subdirectory. Warns on missing table names.
  • Auto-generated README in packets includes an "Included Supplementary Files" table when supplementary CSVs are bundled

Improvements

  • Vignette genenetwork_qtl: chunks now evaluate by default with cached API fallback when GeneNetwork2 is unavailable
  • Vignette single_cell_integration: conditional evaluation no longer requires a pre-existing project directory; only Seurat and ggplot2 are needed

Documentation

  • Vignette locusPackRat_workflow: added "Building Shareable Packets" section with buildPacket() usage and "Including Supplementary CSVs" examples

Package Metadata

  • Exported buildPacket() in NAMESPACE
  • Added data-raw to .Rbuildignore

locusPackRat 0.6.1

Bug Fixes

  • Known Drugs query: Fixed invalid mechanismsOfAction { actionType } field in GraphQL query; now uses mechanismOfAction at the KnownDrug row level (matches current Open Targets API schema)
  • Known Drugs query: Added size: 500 parameter for complete results (default page size truncated output)
  • Pharmacogenomics query: Fixed variantFunctionalConsequence (now SequenceOntologyTerm object) and drug fields (now nested under drugs: [DrugWithIdentifiers!]!); rewrote parser for correct extraction
  • Expression parser: Fixed lapply iterating over data.frame columns instead of rows when fromJSON auto-simplifies; now produces ~180 tissue rows per gene instead of 3 empty rows
  • Mouse Phenotypes parser: Applied same data.frame-to-list-of-rows guard to prevent column iteration bug; renamed targetFromSourceId to targetInModelEnsemblId to match current schema
  • DepMap parser: Fixed column explosion (177 wide-format columns instead of 6) by extracting only expected columns from auto-simplified data.frame
  • QTL credible set gene linking: Expanded id_map to include all ensembl IDs from QTL response (not just project genes), fixing 0/179 match issue in region mode
  • Locus zoom plot path: output_file now accepts only a filename; full paths are reduced to basename() with a warning, preventing nested .locusPackRat/output/<path>/file.pdf output

Improvements

  • generateLocusZoomPlot() supports PNG output via file extension; locus zoom plots display inline in region_qtl_opentargets vignette
  • Reduced batch size to 5 genes when querying heavy data types (mouse_phenotypes, known_drugs) to avoid API timeouts
  • Increased API timeout from 60s to 120s for Open Targets queries
  • Improved parser dual-path handling: data.frame vs list-of-lists detection is now consistent across all data type parsers
  • Audit script now uses name-based file lookup instead of newest-file heuristic, includes row-count validation and locus zoom plot test
  • Vignette genenetwork_qtl: defensive intersect(names(...), expected_cols) column subsetting
  • Vignette region_qtl_opentargets: locus zoom chunks conditionally evaluated when Bioconductor annotation packages are available
  • Vignette single_cell_integration: all chunks conditionally evaluated when Seurat and ggplot2 are installed (fixes R CMD check failure on systems without Seurat)
  • Vignette locusPackRat_workflow: synced VignetteIndexEntry with YAML title

Package Metadata

  • Added Seurat, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db to Suggests
  • Added chr_clean, study_locus_id, study_target_gene_id, and qtl_gene_id to globalVariables() (fixes R CMD check NOTEs)
  • Added .specify and .locusPackRat patterns to .Rbuildignore

locusPackRat 0.6.0

New Features

  • queryOpenTargetsQTL(): Query eQTL, pQTL, and sQTL credible sets from the Open Targets Genetics portal, with locus-to-gene (L2G) prediction scores
  • Expanded queryOpenTargets() data types: now supports diseases, constraints, tractability, expression, mouse_phenotypes, homologues, interactions, known_drugs, depmap, and pharmacogenomics
  • Genome build messaging: initPackRat() now displays a prominent note reminding users that all data must match the project's genome build, with guidance on using rtracklayer::liftOver() for coordinate conversion

New Vignettes

  • region_qtl_opentargets: Region-level QTL analysis using Open Targets eQTL/pQTL data
  • genenetwork_qtl: GeneNetwork2 integration for BXD/DO/HMDP QTL studies
  • single_cell_integration: Single-cell RNA-seq integration via Tabula Muris and Seurat

Removed

  • Removed ComplexUpset dependency (replaced with base R alternatives)

Improvements

  • Added plotgardener citation to locus zoom plot output
  • listPackRatTables(full_info = TRUE) now reports column types, value ranges, and sample counts

locusPackRat 0.5.0

Breaking Changes

  • listPackRatTables(): parameter fullInfo renamed to full_info for API consistency

Improvements

  • Testing infrastructure with testthat
  • Documentation examples for all exported functions
  • Input validation improvements in addRatTable() (validates table_name characters)
  • Match statistics reporting in initPackRat() (shows matched/unmatched genes)
  • GitHub Actions CI for automated R CMD check

locusPackRat 0.4.0

New Features

  • Overlap detection in addRatTable() with overlap_mode parameter for region-based linking
  • removeRatTable() function for removing supplementary tables from projects
  • Column abbreviation feature for Excel output prefixes (avoids column name collisions)
  • Legacy genome support: hg19 and mm10 now available alongside hg38 and mm39
  • queryMouseMine() now uses httr for more reliable API communication
  • Automatic formatting for MouseMine and OpenTargets data in Excel sheet outputs

Bug Fixes

  • Row stripping in makeGeneSheet() only occurs with >= 2 rows present
  • Fix for handling multiple regions in generateLocusZoomPlot()
  • Rare error fix in OpenTargets query response handling

Documentation

  • Updated QTL mapping vignette
  • Improved function documentation and column name descriptions

locusPackRat 0.3.0

  • Initial support for locus zoom plot generation via plotgardener
  • Query functions for external databases (MouseMine, OpenTargets)
  • Project-based workflow with persistent storage

locusPackRat 0.2.0

  • Project directory structure generation
  • Vignette for basic workflow

locusPackRat 0.1.0

  • Initial package release
  • Core functions: initPackRat(), addRatTable(), makeGeneSheet()
  • Support for human and mouse genomes (hg38, mm39)