Changes in version 3.0.3 (2021-11-01) o Removed invariant positions from amino analysis output o Minor formatting changes to output files o Change to CheckRelease based on remote file updates o Differentiate invariant AA positions from invalid AA positions for chisq Changes in version 3.0.2 (2021-10-28) o Added export of Exon to parameters file Changes in version 3.0.1 (2021-10-24) o Adjustment to targeted exon specific amino acid analysis alignment filter o Added known issues section to BIGDAWG vignette Changes in version 3.0.0 (2021-10-23) o Allows for targeted exon specific amino acid analysis, Exon argument Changes in version 2.5.4 (2021-10-21) o Adjustment to amino acid analysis frequency calculator o Few grammatical fixes Changes in version 2.5.3 (2021-10-20) o Adjustment to amino acid analysis frequency calculator o Few grammatical fixes Changes in version 2.5.2 (2021-10-20) o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.46 (2021-10) Build 6c613ce). o Removed p-group reduction for amino acid aligment analysis. Changes in version 2.5.1 (2021-10-19) o Check defined Loci.Set against data. o Few organizational chances to amino acid analysis. No change to functionality. o Few grammatical fixes Changes in version 2.5 (2021-09-09) o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.45.1, 2021-07-12). o Small bug fix in binning algorithm Changes in version 2.4 (2021-06-04) o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.44.0, 2021-04-20). o BIGDAWG now utilizes full length protein sequences (future plan to be exon specific). o Small bug fix in binning algorithm Changes in version 2.3.6 (2021-02-12) o Bug in contextual binning algorithm o Error messages redirected to Std Err. Changes in version 2.3.5 (2021-02-09) o Release v2.3.5 restricted to internal releases o Adjustment to contextual binning algorithm Changes in version 2.3.4 (2021-02-02) o Release v2.3.4 restricted to internal releases o Adjustment of contextual binning algorithm o Fixed bug introduced in L test freq calculations Changes in version 2.3.3 (2021-01-27) o Release v2.3.3 restricted to internal releases o Rework of contextual binning sort and output Changes in version 2.3.2 (2021-01-25) o Release v2.32.2 restricted to internal releases o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.43.0, 2021-01-18). o Fixed bug in counting for some tables with NA values. o Fixed bug in protein alignment generation. o Minor code adjust to CheckRelease() and UpdateRelease() functions. o Added contextual binning to chi square function (Strict.Bin argument). Changes in version 2.3.1 (2020-10-05) o Resubmitted for unarchiving from CRAN. Changes in version 2.3 (2019-10-17) o Changes to NEWS format o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.38.0, 2019-10-17). Changes in version 2.2.1 (2018-09-27) o Fixed bug where passed R object exports to parameter file. o Small changes to console output. Changes in version 2.2 (2018-08-01) o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.33.0, 2018-07-11). Changes in version 2.1.4 (2018-06-22) o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.32.0, 2018-04-16). o Small code fix for updating exon alignment to latest release Changes in version 2.1.3 (2018-02-14) o CheckAllele bug when Trim=T and Res=1 or with 1-Field (2-digit) data. Changes in version 2.1.2 (2018-02-13) o Haplotype ChiSq output bug fix when All.Pairwise=T. Changes in version 2.1.1 (2018-02-09) o GLS to table conversion bug fix - GLSconvert(..,type=GL2Tab). Changes in version 2.1 (2018-02-07) o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.31.0, 2018-01-19). Changes in version 2.0.2 (2017-12-03) o Minor code adjust to CheckRelease() and UpdateRelease() functions. Changes in version 2.0.1 (2017-11-07) o BUG Fix thanks to Rajesh Acharya. o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.30.0, 2017-10-27). o Added dependency for httr package. Changes in version 2.0 (2017-09-15) o Code re-structuring. o The ability to use Gene List Strings via conversion utility, GLSconvert(). o Added GLSconvert Vignette. Changes in version 1.16 (2017-09-05) o Submission to CRAN o Some code re-structuring. o Added parameter check function. o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.29.0.1, 2017-08-18). Changes in version 1.15.3 (2017-08-07) o Now Data argument accepts properly formatted R dataframes (Data=foo). Changes in version 1.15.2 (2017-08-07) o Release v1.15.1 restricted to internal releases. o Fixed miscellaneous bugs specific to HLA data processing. o Now allows for .1, .2, _1, and _2 in column names. o Updates to vignette. Changes in version 1.15 (2017-08-02) o Fixed miscellaneous bugs specific to HLA data processing. o Minor adjustments to code for organization and clarity. Changes in version 1.14.2 (2017-07-18) o Fixed bug where allele names with '00' would be eroneously changed. Changes in version 1.14.1 (2017-07-10) o Minor adjustments to code for organization and clarity. o Fixed bug where sample IDs were not exporting with subject haplotypes. However, they were reported in the same order as the source data. Changes in version 1.14 (2017-07-09) o Adjusted maximum multi-core allowance to 90% of available processor cores. Changes in version 1.13 (2017-07-07) o Submission to CRAN o Minor vignette updates. Changes in version 1.12 (2017-06-21) o Changes in version 1.10 and v1.11 restricted to internal releases. o Transferred github repository location to github.com/IgDAWG/BIGDAWG o Added multi-core capabilities to haplotype analysis to speed up pairwise analysis. Useful for large datasets. o Update to haplotype output files. o Analysis results can be merged into single files with Merge.Output=T. Not recommend for very large datasets and running all pairwise combinations in the haplotype analysis. o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.28.0, 2017-04-13) Changes in version 1.9 (2017-01-20) o Added warning that when All.Pairwise=T or the locus or amino acid tests are run with multiple sets, there will be duplication of analyses and results when sets contain overlapping loci. o When All.Pairwise=T, only pairwise combinations are run in the haplotype analysis. o Changes to output list structure when Return=T. o Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.27.0, 2017-01-20) Changes in version 1.8.4 (2017-01-12) o Naming update to haplotype output files. Haplotype loci will no longer be appended to the filename. When All.Pairwise=T, the filename will be appended with "PairwiseSet" and the set number. A file will also be written to indicate which pairwise set corresponds to which haplotypes. Changes in version 1.8.3 (2016-12-26) o Updated vignette Changes in version 1.8.2 (2016-12-14) o Small adjustments to console output for clarity and grammar. o Moved knitr and rmarkdown from Suggests to Imports. Changes in version 1.8.1 (2016-12-13) o Adjustment to data output merging function. o Small fix to 'A' analysis when output to object. Changes in version 1.8 (2016-12-10) o Added output of merged analyses to main output folder (only when Output = T). Changes in version 1.7 (2016-12-08) o Adjusted function for counting missing alleles to avoid memory limitations. Ported from haplo.stats. Changes in version 1.6 (2016-12-02) o Update bundled IMGT/HLA amino acid exon alignment to latest release (3.26.0.1) o Update to URL for downloading *_prot.txt alignment files o Small fixes to UpdateRelease code when downloading alignment files from IMGT. Changes in version 1.5.8 (2016-12-02) o Fix bug that may be encountered when specifying a set of loci to run. Changes in version 1.5.7 (2016-10-05) o Pandoc requirement for installing from GitHub without RStudio. Thanks to Hugh Salamon. Changes in version 1.5.6 (2016-09-14) o URL change for 'hla_nom_p.txt' download. Thanks to Hugh Salamon. Changes in version 1.5.5 (2016-08-29) o Bug fixed - accidently introduced in v1.5.4 that would cause 'A' test failure Changes in version 1.5.4 (2016-08-26) o Small changes in code organization. o Update bundled IMGT/HLA amino acid exon alignment to latest release (3.25.0) Changes in version 1.5.3 (2016-08-25) o Fix bug in UpdateRelease() on some installations. Changes in version 1.5.2 (2016-08-03) o Fix for an incorrect error message wording. Thanks to Farrel Buchinsky. o Fix for data read-in when 1-Field resolution. Thanks to Farrel Buchinsky. Changes in version 1.5.1 (2016-06-20) o Bug fix in output list. Changes in version 1.5.0 (2016-06-15) o BIGDAWG can now return results as list with parameter Return=T. o Minimize console output with Verbose=F. o Turn off write results to file with Output=F. o Bug fix for DRB3/4/5 parsing with NA's. Changes in version 1.4.0 (2016-05-12) o Version change, submission to CRAN. Changes in version 1.3.9 (2016-05-11) o Vignette link modifications. o Bug fix for UpdateRelease() when there is no internet connection. Changes in version 1.3.8 (2016-05-04) o Error message for allele formatting imbalance across loci when HLA=T. Changes in version 1.3.7 (2016-04-29) o Bug fix for CheckRelease() when there is no internet connection. o Bug fix when setting Output=F, for testing only. o Bug fix HWE displaying control analysis twice. o Minor changes to vignette. o Adjust Errors to only print out when Output=T. Changes in version 1.3.6 (2016-04-26) o Added function to check Changes in version ersion and IMGT/HLA version simultaneously using CheckRelease(). o Removed UpdateRelease(GetRelease). See vignette. o Vignette update to reflect changes. Changes in version 1.3.5 (2016-04-20) o Minor wording change to vignette to enhance clarity and reflect GitHub availability. o Added function to check release BIGDAWG uses for IMGT/HLA database. See vignette. o Added Hardy Weinberg Equilibrium testing for cases. Useful when employing other binary phenotypes. o Update bundled IMGT/HLA amino acid exon alignment to latest release (3.24.0) Changes in version 1.3.4 (2016-04-08) o Added output of subject haplotypes to file when running haplotype analysis. o Bug fix in haplotype generation and outputs. o Bug fix in when locus has only a single allele. Thanks go to Antoine Lizee. o Other minor improvements to enhance data processing. o Minor wording change to vignette to enhance clarity. o Updated Human Immunology paper to BIGDAWG. o Added ability to read in HLA data when DRB3, DRB4, and DRB5 are collapsed to a single column. DR haplotypes are parsed accordingly. See vignette for details. o Added output of Sample IDs removed due to missing alleles exceeding set threshold. o Adjusted Missing default to 2. o When running multiple locus sets the for haplotype analysis, now displays which haplotype is being run. Changes in version 1.2.8 (2016-02-28) o Bug fix. Changes in version 1.2.7 (2016-02-27) o Bug fix for chi square output using some data sets. Changes in version 1.2.6 (2016-02-19) o BIDAWG v1.2.1 - v1.2.5 unreleased internal versions. o Bug fix when removing missing data as set by 'Missing' parameter. Thanks go to Arun Khattri. o Added reference to BIGDAWG publication in DESCRIPTION and vignette. o Update bundled IMGT/HLA amino acid exon alignment to latest release (3.23.0) Changes in version 1.2.1 (2015-11-09) o Added NEWS file to document BIGDAWG releases. o Bug fix when EVS.rm was set to TRUE. o Precheck.txt renamed to Data_Summary.txt. o Distinction between Run parameters and Set parameters. o Run Parameters generated and written to file earlier in script. o Added section delimiter for 'Data Processing And Checks' in console output. o Changes in wording for select BIGDAWG error messages. o Update to Hardy-Weinberg test. o Update bundled IMGT/HLA amino acid exon alignment to latest release (3.22.0)