NEWS.md

In RajLabMSSM/echofinemap: echoverse module: Fine-mapping functions

echofinemap 0.99.5

New features

• Implement rworkflows

echofinemap 0.99.4

New features

• Pass more arg down to method-level via finemap_args.
• Add check_args function to handle finemap_args.
• Offload piggyback functions to echodata (echodata::get_data)
• SUSIE:
  • Condense manual_var_y and var_name into one arg: var_y
  • Replace dataset_type with more appropriate case_control arg.
• Fully documented all functions.
• Remove POLYFUN_plot (redundant code with echoplot)
• POLYFUN_: fixed or deleted functions
  • POLYFUN_munge_summ_stats
  • POLYFUN_compute_priors

Bug fixes

• Make Rfast an Import to avoid downstream issues with echolocatoR.
• Fix GHA: @master --> @v2
• Remove unnecessary deps:
  • ggplot2
• Adjust .Rbuildignore to not cause issues with large inst/tools subfolder.
• require_cols:
  • Now takes the more accurate case_control arg instead of dataaset_type.

echofinemap 0.99.3

New features

• COJO:
  • Now working with echoverse.
  • Added 3 COJO modes to list of finemapping methods: run_stepwise,run_conditional,run_joint
  • Automated installation of GCTA.
  • Added unit tests.
• PAINTOR:
  • Now working with echoverse.
  • Generalized to any data input type (GWAS/QTL/TWAS) to avoid hard-coded args.
  • Streamlined functions and reduced clutter.
  • Automated installation of PAINTOR.
  • Can now handle multi-trait and multi-ancestry fine-mapping.
  • Added unit tests.
• multifinemap:
  • Automatically checks finemap_methods
  • Passes seed all the way to finemapping functions.
  • Expanded finemapping methods.
• check_required_cols: Add coloring via cli.
• required_cols: Add URLS to GitHub repos and citations.
• Added functions for checking each fine-mapping CLI method's version:
  • <method>_check_version
  • Changed POLYFUN_find_polyfun_folder --> POLYFUN_find_folder for consistency.

Bug fixes

• FINEMAP: Figured out solution to get FINEMAP v1.4 working on Mac. Instructions in messages now updated.
• create_method_path: Use basename(LD_reference) for file naming.
• Require "MAF" columns for coloc, as it now seems to be required by the error message when it's missing: dataset : please give MAF if using p values

echofinemap 0.99.2

New features

• Updated GHA.
• POLYFUN:
  • Can now use FINEMAP or SUSIE as a method.
  • Change column "POLYFUN_h2" --> "POLYFUN.h2" to make consistent with other cols.
  • Automatically installs itself from the GitHub submodule.
  • POLYFUN_help now exported.
• Use Rfast to speed up SUSIE.
• remove_na_rows: Remove rows with NAs in tool-specific essential cols.
• Update FINEMAP to v1.4.1.
• Make separate columns for FINEMAP results:
  • PP: Conditional PP (from .cred file(s))
  • PP_snp: Marginal PP (from .snp file)
  • PP_config: Configuration PP (from .config file)
  • k: Optimized number of causal SNPs (<= n_causal).
• Got FINEMAP to use priors via data.k file.

Bug fixes

• Switch SUSIE method from susie_suff_stat to susie_rss for parameter consistency.
• Fix ABF.
  • Use mean proportion_cases
• Test FINEMAP v1.4 and v1.3.1 on Linux.
• Actually pass force_new_finemap all the way down.
• Dynamically infer "data.cred*" file name.
• Fill NAs in FINEMAP CS/PP.
• SUSIE:
  • susieR v0.11 contained serious bugs that caused susie_rss to fail. This was fixed in v0.12 (which is now a version requirement for echofinemap). See here for details: https://github.com/stephenslab/susieR/issues/167

echofinemap 0.99.1

New features

• Updated conda env to echoR_mini.
• Add prior_k as argument to FINEMAP.
• Add message about gcc8 to FINEMAP v1.4 error.

Bug fixes

• Minor fixes to POLYFUN method checks.

echofinemap 0.99.0

• Added a NEWS.md file to track changes to the package.

RajLabMSSM/echofinemap documentation built on Jan. 3, 2023, 1:42 a.m.