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catalogueR 2.0.1

Bug fixes

  • Add skip_on_cran() and skip_if_offline() to test-COLOC_run to prevent hard failures on CI when piggyback downloads are unavailable.
  • Fix hardcoded $POS in test-eQTLcatalogue_fetch — now detects position column dynamically (POS or BP).
  • Fix construct_locus_name() to detect position column dynamically.
  • Add "aut" role to maintainer in DESCRIPTION (required by --as-cran).

catalogueR 2.0.0

New features

  • Remove 15 deprecated function wrappers that have been deprecated since v1.0.x.

Bug fixes

  • Fix dataset_id column detection in eQTL Catalogue queries.
  • Fix data.table recycling warnings.
  • Update R requirement from >= 3.6 to >= 4.1.
  • Remove unused imports: echoconda, stringr, utils, rlang.
  • Rd: convert \itemize to \describe for named lists, citEntry to bibentry, bare doi URLs to \doi{}, title case.

catalogueR 1.0.3

Bug fixes

  • Local R CMD check fixes and compatibility updates.

catalogueR 1.0.2

Bug fixes

  • Standardize rworkflows.yml with canonical template: enable Docker on ghcr.io, set write-all permissions, use GITHUB_TOKEN, add devel branch trigger.
  • Update R requirement from >= 3.6.0 to >= 4.1.
  • Remove tracked .DS_Store files.

catalogueR 1.0.1

New features

  • Implement rworkflows.

catalogueR 1.0.0

New features

  • Offload functions to echoverse deps:
    • get_data() --> echodata
    • get_os() --> echodata
    • load_rdata() --> downloadR
    • example_sumstats_paths() --> echpdata::get_Nalls2019_loci()
    • find_consensus_SNPs --> echodata::find_consensus_snps()
    • locus_plot --> echoplot
  • Rename functions to fit echoverse conventions:
    • Remove "." from any function names.
    • All eQTL Catalogue functions start with eQTLcatalogue_.
    • All COLOC functions start with COLOC_.
    • Deprecated all functions properly to let users know.
  • Change arg in all functions:
    • gwas_data --> query_granges
    • genome_build --> query_genome
  • Condensed multiple arguments into echotabix::construct_query()
    • gwas.data, chrom, bp_min, bp_max
  • New exported functions:
    • COLOC_heatmap
    • COLOC_corplot

Bug fixes

  • Updated function/arg names from echoverse deps.
  • Updated meta data to include latest paths and datasets.
  • fix_ftp: Replacing "ftp:" prefix with "http:" seems to drastically improve the ability of functions to query the files.

catalogueR 0.1.1

New features

  • Added a NEWS.md file to track changes to the package.
  • Split functions into separate files.
  • Made README into .Rmd file.
  • Changed license to GPL-3 and removed LICENSE file.
  • Removed old data.table version requirement (issues with compressed files have since been resolved).
  • Updated .Rbuildignore and .gitignore
  • Added GitHub Actions via biocthis::use_bioc_github_action(pkgdown_covr_branch = c("main","master")).
  • Replaced T/F with TRUE/FALSE in accordance with best coding practices.
  • Replaced NAMESPACE file with Roxygen-generated version.
  • Replaced internal functions with echoverse packages:
    • echotabix
    • echoconda
  • Replaced built-in datasets with echodata datasets:
    • BST1
    • LRRK2
    • MEX3C
  • Styled code with: styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
  • Replace printer with messager.
  • Created dev branch.
  • Add GTEX_v8 metadata to eQTL_Catalogue.list_datasets.
  • Example coloc results now accessed via get_coloc_QTLs:
    • Moved coloc_QTLs_full to Releases as it was >12Mb.
    • Moved coloc_QTLs to Releases as it was >1.5Mb.
  • Moved eQTL Catalogue query results to Release via example_eQTL_Catalogue_query_paths.
  • Replace liftover functions with echotabix::liftover (removed unused deps).
  • Replaced rsids_from_coords with echodata::coords_to_rsids (removed unused deps).
  • Made "REST" default method for all relevant functions.
  • Deprecated:
    • gather_files in favor of more descriptive merge_files
    • gather_colocalized_data in favor of more descriptive merge_colocalized_data

Bug fixes

  • Reduced NAMESPACE by properly exporting functions.
  • Removed library calls within functions.
  • Added requireNamespace where suggests are used.
  • Changed eQTL_Catalogue.query so that the default is use_tabix=FALSE due to instability of using tabix with the EBI server. See here for details.
  • run_coloc automatically infers (effective) sample size and checks that MAF is present for all SNPs (after removing MAF>=1 or <=0 or ==NA).
  • Removed example query results (e.g. MEX3C__Alasoo_2018.macrophage_IFNg) from built-in data as these were already included in exdata.

catalogueR 0.1.0

First version of catalogueR created as a sister package of echolocatoR.