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genbin 0.0.0.9000 (2021-08-14)

  • First version of various functions organized around this package!
    • Original (scripts in a private repository, not a proper package) was not tested systematically, and evolved slowly so many features were only partially present in newer code while older code did things in more awkward ways.
    • New code shares the way errors are handled across all cases; style is more coherent, including option names, behaviors, parsers, etc.
  • This early version is thoroughly tested, but not documented at all. No functions are exported.

genbin 0.0.1.9000 (2021-08-16)

  • Documented and exported all main functions!
  • Package passes checks!

genbin 0.0.2.9000 (2021-08-17)

  • Added package documentation page and README.md with sample pipelines for GCTA and plink PCA.
  • Function gcta_mlma expanded documentation to explain which errors cause function to return NULL instead of stopping.
  • Function plink_glm expanded documentation to include delete_files_log under seealso section.

genbin 0.0.3.9000 (2021-09-20)

  • Function plink_glm added option vif.
  • DESCRIPTION added github links (URL, BugReports).
  • README.md cleaned install instructions

genbin 0.0.4.9000 (2022-05-25)

  • Reversed ref and alt alleles in all association test parser functions
    • In line with the same change in genio::read_bim.
    • Original interpretation of ref and alt was wrong, it has now been corrected.
    • Functions affected: read_bolt_lmm, read_gcta_mlma, read_gemma_assoc, read_plink_glm, and their downstream dependencies bolt_lmm, gcta_mlma, gemma_lmm, plink_glm.
  • Function read_gcta_hsq and its dependency gcta_reml debugged
    • Fixed parser warning by limiting the number of lines to read to the first 4 (excluding header), so now the $data component of its return list will be more limited.

genbin 0.0.5.9000 (2022-05-25)

  • Function plink_glm added option max_corr.

genbin 0.0.6.9000 (2022-12-07)

  • Function gcta_mlma added option file_covar_cat.
  • Removed LazyData: true from DESCRIPTION

genbin 0.0.7.9000 (2023-05-11)

  • Added functions plink_hardy, read_plink_hardy, and delete_files_plink_hardy to run plink2 --hardy, read, and delete its output, respectively.

genbin 0.0.8.9000 (2023-05-11)

  • Function plink_hardy added midp option.
  • Function read_plink_hardy supports midp output, renaming final column from "midp" to "p".

genbin 0.0.9.9000 (2024-11-09)

  • Function read_plink_glm (and its dependency plink_glm) updated parser to work with latest plink2 outputs, while retaining backward compatibility to previous format.
  • Function gcta_reml added option m_pheno that allows specifying the phenotype index in a file with multiple phenotypes.

genbin 0.0.10.9000 (2025-08-13)

  • Function gcta_reml added options file_covar and file_covar_cat to provide covariates to this heritability analysis.