NEWS.md

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

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.

RajLabMSSM/echoLD documentation built on May 12, 2024, 3:23 a.m.