NEWS.md

In OchoaLab/genbin: R wrappers for binaries in genetics

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.

OchoaLab/genbin documentation built on Nov. 14, 2024, 7:33 p.m.