NEWS.md

In richelbilderbeek/plinkr: Interface to PLINK

News

Newest versions at top.

plinkr v0.20.3 (unreleased)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.20.2 (2022-05-19)

NEW FEATURES

• Add 'pca'
• Add 'plot_pca_results'

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.20.1 (2021-05-04)

NEW FEATURES

• Add 'check_sample_selector'
• Add 'check_single_sample_selector'
• Add 'create_keep_args'
• Add 'create_random_samples_selector'
• Add 'create_select_samples_args'
• Add 'create_select_single_sample_args'
• Add 'create_selected_sample_ids'
• Add 'create_single_sample_selector'
• Add 'create_test_single_sample_selector'
• Add 'get_n_samples'
• Add 'is_fam_table'
• Add 'is_psam_table'
• Add 'is_single_sample_selector'
• Add 'select_samples'
• Can use the PLINK '--allow-no-sex' flag in 'assoc_qt'
• Can use the PLINK '--ci' flag in 'assoc_qt'

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.20 (2022-04-26)

NEW FEATURES

• Add 'select_snps'
• Add 'create_chromosome_selector'
• Add 'create_single_snp_selector'
• Add 'create_random_snps_selector'
• Add 'create_snp_range_selector'
• Add 'create_snp_window_selector'
• Use attributes to distinguish between pgen_table and bed_table

MINOR IMPROVEMENTS

• 'assoc' now follows uniform interface

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Uses genio v1.1.0

plinkr v0.19.2 (2022-03-15)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• 'assoc_qt_params' has no 'data' nor 'phe_table' anymore, as these are part of 'assoc_qt_data'

plinkr v0.19.1 (2022-03-08)

NEW FEATURES

• Added 'check_phe_file_ok_for_qt'
• Added 'check_phe_table_ok_for_qt'
• Added 'get_n_snps'
• Added 'get_n_snps_from_bed_table'
• Added 'get_n_snps_from_bim_table'
• Added 'get_n_snps_from_map_table'
• Added 'get_n_snps_from_ped_table'
• Added 'get_n_snps_from_pgen_table'
• Added 'get_n_snps_from_pvar_table'
• Added 'is_bed_table'
• Added 'is_bim_table'
• Added 'is_map_table'
• Added 'is_ped_table'
• Added 'is_pgen_table'
• Added 'is_pvar_table'

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Added 'check_phe' does not check if a table of phenotypic values can be used in a quantitative trait analysis

plinkr v0.19 (2022-02-25)

NEW FEATURES

• Use 'rocker/tidyverse' as the base for the Singularity container

MINOR IMPROVEMENTS

• Improve Singularity doc

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.18.0.3 (2022-02-22)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• A phenotype table's IID is of type character

DEPRECATED AND DEFUNCT

• None

plinkr v0.18.0.2 (2022-02-21)

NEW FEATURES

• Added 'check_fam_filename'
• Added 'check_phe_filename'
• Added 'check_sample_ids'
• Added 'check_sample_ids_filename'
• Added 'get_marker_correlation_coefficients'
• Added 'get_minor_alelle_frequencies'
• Added 'get_sample_ids_from_fam_file'
• Added 'get_sample_ids_from_fam_table'
• Added 'get_sample_ids_from_phe_file'
• Added 'get_sample_ids_from_phe_table'
• Added 'get_test_sample_ids'
• Added 'keep'
• Added 'save_sample_ids'

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.18.0.1 (2022-01-13)

NEW FEATURES

• Added convert_plink_bin_files_to_plink_text_files
• Added rename_fids to rename all family IDs in any in-memory data
• Added rename_iids to rename all within-family IDs in any in-memory data

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.18 (2021-11-02)

NEW FEATURES

• Uniform interface

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Renamed create_demo_assoc_qt_params to create_demo_assoc_qt_data
• Removed assoc_qt_nth_trait

plinkr v0.17.1 (2021-10-04)

NEW FEATURES

• Added 'compare_assoc_qt_speed' to compare speed of PLINK versions and types of data, #26
• Check PLINK arguments to give an error for commands that are ignored, as PLINK will not always give you an error or warning

MINOR IMPROVEMENTS

• Use stringi version v1.7.5, #21
• Simplify some get_test_ functions
• Improve code coverage

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.17 (2021-10-01)

NEW FEATURES

• Can convert PLINK2 binary files to PLINK1 binary files
• Can do assoc_qt with PLINK2 binary data

MINOR IMPROVEMENTS

• pgen_table can have SNP IDs as column names and individuals' IDs as row names

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Remove redundant 'to_file' in 'save[something]' function names

plinkr v0.16.2 (2021-09-28)

NEW FEATURES

• Can convert PLINK1 text files to PLINK1 binary files to PLINK2 binary files

MINOR IMPROVEMENTS

• None

BUG FIXES

• stringi::stri_trim_both and stringi::stri_split_regex sometimes gives an 'embedded nul in string' error or a segfault. This has been reported at https://github.com/gagolews/stringi/issues/458. Until then, a workaround with base R is used

DEPRECATED AND DEFUNCT

• None

plinkr v0.16.1 (2021-09-23)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• stringr::str_trim sometimes gives an 'embedded nul in string' error. This has been reported at https://github.com/tidyverse/stringr/issues/399. Until then, a workaround is used

DEPRECATED AND DEFUNCT

• None

plinkr v0.16 (2021-09-22)

NEW FEATURES

• Use a data function argument, that can be either be PLINK1 text data (read from .ped and .map files), PLINK 1 binary data (read from .bed, .bim and .fam files) or PLINK2 binary data (not yet implemented)

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.15.2 (2021-07-30)

NEW FEATURES

• Nonse

MINOR IMPROVEMENTS

• Singularity container is tested to run plinkr scripts

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.15.1 (2021-07-28)

NEW FEATURES

• Nonse

MINOR IMPROVEMENTS

• None

BUG FIXES

• Singularity version matches package version

DEPRECATED AND DEFUNCT

• None

plinkr v0.15 (2021-07-28)

NEW FEATURES

• Added a Singularity container with plinkr and the PLINKs installed
• Start of using the three types of data: create_plink_text_data, create_plink_bin_data and create_plink2_bin_data

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.14 (2021-07-01)

NEW FEATURES

• Add vignette with PLINK tutorial
• Add install_plink_tutorial_data and uninstall_plink_tutorial_data to install and uninstall the PLINK tutorial data
• Add read_plink_assoc_adjusted_file to read PLINK .assoc.adjusted files
• Add read_plink_lmiss_file to read PLINK .lmiss files
• Add read_plink_imiss_file to read PLINK .imiss files
• Add read_plink_frq_file to read PLINK .frq files
• Add read_plink_frq_strat_file to read PLINK .frq.strat files
• Add missing_from_bfile to run a PLINK --missing analysis from PLINK binary files
• Add freq_from_bfile to run a PLINK --freq analysis from PLINK binary files
• Add freq_from_bfile_within_phe_file to run a PLINK --freq analysis from PLINK binary files with a stratification on the phenotype
• Add assoc_from_bfile to run a PLINK --assoc analysis from PLINK binary files
• Add assoc_adjust_from_bfile to run a PLINK --assoc --adjust analysis from PLINK binary files
• Add assoc_qt_covar to do a quantitative traits analysis with covariates

MINOR IMPROVEMENTS

• Add vignette to demonstrate how example files are created
• Use --noweb flag only in PLINK versions that support it

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• All function with phenotype in it (e.g. read_phenotype_file), use phe instead (e.g. read_phe_file). This to have a naming scheme consistent with PLINK
• assoc_ functions return a list with an association table and a log (instead of just the association table), to ensure all info by PLINK is used
• Example phenotype files with the .raw extension have been renamed to have a .phe file extension, except for pheno.raw, as that filename is used in the PLINK tutorial

plinkr v0.13 (2021-06-17)

NEW FEATURES

• Phenotype files can have phenotype names

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.12 (2021-06-16)

NEW FEATURES

• Can read .bed, .bim and .fam files
• Check that maximally 95 chromosomes are used, as this is a (default) PLINK limit, see https://www.cog-genomics.org/plink/1.9/input#chr_set
• Handle multiple phenotypes using in the PLINK way, using --all-pheno
• Add save_qassoc_table to save the results of a quantitive association to file in the same way PLINK creates a .qassoc file
• Renamed column names family_id to FID, as this is the abbreviation PLINK uses, see https://www.cog-genomics.org/plink/1.9/input#pheno
• Renamed column names within_family_id to IID, as this is the abbreviation PLINK uses, see https://www.cog-genomics.org/plink/1.9/input#pheno

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.11 (2021-06-09)

NEW FEATURES

• Add confidence interval for assoc
• read_plink_assoc_file can read .assoc files with a confidence interval
• Add make_bed to convert the (non-binary) .map and .ped files to their binary .bed, .bim and .fam equivalents

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.10 (2021-06-02)

NEW FEATURES

• install_plinks also installs PLINK2

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.9 (2021-05-31)

NEW FEATURES

• Add assoc to detect associations for a binary trait
• Allow to use a custom version of PLINK, #4, thanks @HadrienG
• Can run PLINK on Mac, #5, thanks @HadrienG

MINOR IMPROVEMENTS

• create_demo_assoc_qt_params can now accept multiple additive and epistatic traits
• All temporary files are cleaned up

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Functions that call PLINK must use a plink_options parameter

plinkr v0.8 (2021-5-27)

NEW FEATURES

• Add tri- and quadallelic traits
• Add epistatic trait

MINOR IMPROVEMENTS

• PLINK warnings are detected and put into R warning

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.7 (2021-05-27)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Improved interface of ´create_demo_assoc_qt_params´

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.6 (2021-05-26)

NEW FEATURES

• First version of ´create_demo_assoc_qt_params´ to nicely demonstrate a quantitative trait analysis

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

plinkr v0.5 (2021-05-26)

NEW FEATURES

• run_plink is stable
• Ready for users

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

richelbilderbeek/plinkr documentation built on March 25, 2024, 3:18 p.m.