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echoLD 1.0.0

New features

  • Remove deprecated load_or_create() wrapper.

Bug fixes

  • Fix missing scipy/requests in reticulate Python environment for UKB LD queries.
  • Remove stray 1KG tabix index committed to repo.
  • Skip local VCF tests when Rsamtools can't read bundled VCF.
  • Fix Rd formatting and \dontrun{} example guards.
  • Add Rplots.pdf and *.tbi to .gitignore.

echoLD 0.99.12

Bug fixes

  • Local R CMD check fixes and compatibility updates.

echoLD 0.99.11

New features

  • Standardize rworkflows.yml with canonical template: enable Docker on ghcr.io, set write-all permissions, use GITHUB_TOKEN, add devel branch trigger.
  • Remove tracked .DS_Store files.

echoLD 0.99.10

New features

  • get_LD: pass up subset_common arg

Bug fixes

  • Fix UKB LD now that AlkesGroup moved data to AWS S3 bucket: #12

echoLD 0.99.9

New features

  • Implement rworkflows

echoLD 0.99.8

New features

  • get_UKB_MAF --> get_MAF_UKB
  • get_LD_UKB:
    • New subfunction load_ld_r``tryFun:
    • Remove tryFun function.

Bug fixes

  • Added echoconda to Remotes: github::RajLabMSSM/echoconda
  • Remote GenomeInfoDb Import (no longer used here).
  • Fix GHA: @master --> @v2
  • Fix saveSparse example.
  • Fix filter_LD unit test.
  • Fix download_UKB_LD: Update downloadR::downloader arg from output_path --> output_dir

echoLD 0.99.7

New features

  • New function:
    • vcf_to_plink
  • New exports:
    • readSparse
    • saveSparse
    • get_LD_vcf
    • get_LD_matrix
    • r2_to_r
    • to_sparse
  • Enabled reading of pre-computed matrices stored in various file formats, both from local and remote files.

Bug fixes

  • Pass query_genome to get_LD_vcf() and get_LD_matrix.

echoLD 0.99.6

New features

  • Perform liftover in all areas where necessary.
  • Confirm that UKB is indeed aligned to hg19.
  • Document genome builds of each LD reference panel.

Bug fixes

  • Fix typos in unit tests: test-plot_LD/
  • Remove R.utils from Imports.

echoLD 0.99.5

New features

  • Updated GHA.

Bug fixes

  • Flipped reporting of SNPs/samples in compute_LD.

echoLD 0.99.4

New features

  • Switched default conda env to echoR_mini.
  • Make dedicated read_LD_list.

Bug fixes

  • Change default method for echotabix::query_vcf to "conda" while "variantannotation" is being fixed.
  • Move extdata example VCFs to echodata.
  • Ensure get_LD converts returned matrix to sparse for all methods.
  • Pass conda_env down to get_LD_custom.

echoLD 0.99.3

Bug fixes

  • Fix downloadR.
  • Fix which package load_ld.py is imported from (echodata --> echoLD).
  • Remove copy of dt_to_granges.

echoLD 0.99.2

New features

  • Update to match changes in echotabix.
  • Change to more consistent/intuitive function names:
    • create_or_load --> get_LD
    • LD_ukbiobank --> get_LD_UKB
    • LD_1KG --> get_LD_1KG
    • LD_custom --> get_LD_custom

echoLD 0.99.1

New features

  • Added more unit tests.
  • Exported:
    • filter_LD
    • subset_common_snps
    • plot_LD
  • Moved Imports to Suggests:
    • gaston
    • graphics
    • LDlinkR
    • adjclust
  • get_UKB_MAF: Cached UKB MAF in echoLD-specific cache.
  • Moved majority of data to echodata package.
  • Convert LD to sparse by default. Only convert if not already sparse.
  • Remove codecov yaml.
  • Add CITATIONS file.
  • Update README to use autofill.
  • Add hex sticker.
  • Remove docs/
  • Updated GHA with latest ``templateR` workflow.

echoLD 0.99.0

New features

  • Added a NEWS.md file to track changes to the package.
  • Utilises echoannot and downloadR packages.