NEWS

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BIGDAWG 3.0.8

• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.53, 2023-07) o

BIGDAWG 3.0.7

• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.52.0, 2023-04)
• Bug fix for certain data tables

BIGDAWG 3.0.6

• Adjustment for data table read-ins
• Name change in an IMGT/HLA file
• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.50.0, 2022-10)
• Calculation adjustment for Odds Ratio Tables. Thanks to Ben Solomon.

BIGDAWG 3.0.5

• Bug identified when using EVS.rm = T

BIGDAWG 3.0.4

• Bug identified when using R > v4.1
• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.49, 2022-07).
• Adjustment to A test for reporting to file

BIGDAWG 3.0.3 (2021-11-17)

• Removed invariant positions from amino analysis output
• Minor formatting changes to output files
• Change to CheckRelease based on remote file updates
• Differentiate invariant AA positions from invalid AA positions for chisq

BIGDAWG 3.0.2

• Added export of Exon to parameters file

BIGDAWG 3.0.1

• Adjustment to targeted exon specific amino acid analysis alignment filter
• Added known issues section to BIGDAWG vignette

BIGDAWG 3.0.0

• Allows for targeted exon specific amino acid analysis, Exon argument

BIGDAWG 2.5.4

• Adjustment to amino acid analysis frequency calculator
• Few grammatical fixes

BIGDAWG 2.5.3

• Adjustment to amino acid analysis frequency calculator
• Few grammatical fixes

BIGDAWG 2.5.2

• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.46 (2021-10) Build 6c613ce).
• Removed p-group reduction for amino acid aligment analysis.

BIGDAWG 2.5.1

• Check defined Loci.Set against data.
• Few organizational chances to amino acid analysis. No change to functionality.
• Few grammatical fixes

BIGDAWG 2.5

• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.45.1, 2021-07-12).
• Small bug fix in binning algorithm

BIGDAWG 2.4

• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.44.0, 2021-04-20).
• BIGDAWG now utilizes full length protein sequences (future plan to be exon specific).
• Small bug fix in binning algorithm

BIGDAWG 2.3.6 (2021-02-11)

• Bug in contextual binning algorithm
• Error messages redirected to Std Err.

BIGDAWG 2.3.5

• Release v2.3.5 restricted to internal releases
• Adjustment to contextual binning algorithm

BIGDAWG 2.3.4

• Release v2.3.4 restricted to internal releases
• Adjustment of contextual binning algorithm
• Fixed bug introduced in L test freq calculations

BIGDAWG 2.3.3

• Release v2.3.3 restricted to internal releases
• Rework of contextual binning sort and output

BIGDAWG 2.3.2

• Release v2.32.2 restricted to internal releases
• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.43.0, 2021-01-18).
• Fixed bug in counting for some tables with NA values.
• Fixed bug in protein alignment generation.
• Minor code adjust to CheckRelease() and UpdateRelease() functions.
• Added contextual binning to chi square function (Strict.Bin argument).

BIGDAWG 2.3.1 (2020-10-08)

• Resubmitted for unarchiving from CRAN.

BIGDAWG 2.3 (2019-11-12)

• Changes to NEWS format
• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.38.0, 2019-10-17).

BIGDAWG 2.2.1

• Fixed bug where passed R object exports to parameter file.
• Small changes to console output.

BIGDAWG 2.2

• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.33.0, 2018-07-11).

BIGDAWG 2.1.4

• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.32.0, 2018-04-16).
• Small code fix for updating exon alignment to latest release

BIGDAWG 2.1.3

• CheckAllele bug when Trim=T and Res=1 or with 1-Field (2-digit) data.

BIGDAWG 2.1.2

• Haplotype ChiSq output bug fix when All.Pairwise=T.

BIGDAWG 2.1.1

• GLS to table conversion bug fix - GLSconvert(..,type=GL2Tab).

BIGDAWG 2.1 (2018-02-08)

• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.31.0, 2018-01-19).

BIGDAWG 2.0.2

• Minor code adjust to CheckRelease() and UpdateRelease() functions.

BIGDAWG 2.0.1

• BUG Fix thanks to Rajesh Acharya.
• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.30.0, 2017-10-27).
• Added dependency for httr package.

BIGDAWG 2.0

• Code re-structuring.
• The ability to use Gene List Strings via conversion utility, GLSconvert().
• Added GLSconvert Vignette.

BIGDAWG 1.16 (2017-09-06)

• Submission to CRAN
• Some code re-structuring.
• Added parameter check function.
• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.29.0.1, 2017-08-18).

BIGDAWG 1.15.3

• Now Data argument accepts properly formatted R dataframes (Data=foo).

BIGDAWG 1.15.2

• Release v1.15.1 restricted to internal releases.
• Fixed miscellaneous bugs specific to HLA data processing.
• Now allows for .1, .2, _1, and _2 in column names.
• Updates to vignette.

BIGDAWG 1.15

• Fixed miscellaneous bugs specific to HLA data processing.
• Minor adjustments to code for organization and clarity.

BIGDAWG 1.14.2 (2017-07-19)

• Fixed bug where allele names with '00' would be eroneously changed.

BIGDAWG 1.14.1

• Minor adjustments to code for organization and clarity.
• Fixed bug where sample IDs were not exporting with subject haplotypes. However, they were reported in the same order as the source data.

BIGDAWG 1.14 (2017-07-10)

• Adjusted maximum multi-core allowance to 90% of available processor cores.

BIGDAWG 1.13 (2017-07-08)

• Submission to CRAN
• Minor vignette updates.

BIGDAWG 1.12

• Changes in version 1.10 and v1.11 restricted to internal releases.
• Transferred github repository location to github.com/IgDAWG/BIGDAWG
• Added multi-core capabilities to haplotype analysis to speed up pairwise analysis. Useful for large datasets.
• Update to haplotype output files.
• 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.
• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.28.0, 2017-04-13)

BIGDAWG 1.9

• 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.
• When All.Pairwise=T, only pairwise combinations are run in the haplotype analysis.
• Changes to output list structure when Return=T.
• Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.27.0, 2017-01-20)

BIGDAWG 1.8.4

• 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.

BIGDAWG 1.8.3

• Updated vignette

BIGDAWG 1.8.2

• Small adjustments to console output for clarity and grammar.
• Moved knitr and rmarkdown from Suggests to Imports.

BIGDAWG 1.8.1

• Adjustment to data output merging function.
• Small fix to 'A' analysis when output to object.

BIGDAWG 1.8

• Added output of merged analyses to main output folder (only when Output = T).

BIGDAWG 1.7

• Adjusted function for counting missing alleles to avoid memory limitations. Ported from haplo.stats.

BIGDAWG 1.6

• Update bundled IMGT/HLA amino acid exon alignment to latest release (3.26.0.1)
• Update to URL for downloading *_prot.txt alignment files
• Small fixes to UpdateRelease code when downloading alignment files from IMGT.

BIGDAWG 1.5.8

• Fix bug that may be encountered when specifying a set of loci to run.

BIGDAWG 1.5.7

• Pandoc requirement for installing from GitHub without RStudio. Thanks to Hugh Salamon.

BIGDAWG 1.5.6

• URL change for 'hla_nom_p.txt' download. Thanks to Hugh Salamon.

BIGDAWG 1.5.5 (2016-08-31)

• Bug fixed - accidently introduced in v1.5.4 that would cause 'A' test failure

BIGDAWG 1.5.4 (2016-08-28)

• Small changes in code organization.
• Update bundled IMGT/HLA amino acid exon alignment to latest release (3.25.0)

BIGDAWG 1.5.3

• Fix bug in UpdateRelease() on some installations.

BIGDAWG 1.5.2

• Fix for an incorrect error message wording. Thanks to Farrel Buchinsky.
• Fix for data read-in when 1-Field resolution. Thanks to Farrel Buchinsky.

BIGDAWG 1.5.1

• Bug fix in output list.

BIGDAWG 1.5.0

• BIGDAWG can now return results as list with parameter Return=T.
• Minimize console output with Verbose=F.
• Turn off write results to file with Output=F.
• Bug fix for DRB3/4/5 parsing with NA's.

BIGDAWG 1.4.0 (2016-05-14)

• Version change, submission to CRAN.

BIGDAWG 1.3.9

• Vignette link modifications.
• Bug fix for UpdateRelease() when there is no internet connection.

BIGDAWG 1.3.8

• Error message for allele formatting imbalance across loci when HLA=T.

BIGDAWG 1.3.7

• Bug fix for CheckRelease() when there is no internet connection.
• Bug fix when setting Output=F, for testing only.
• Bug fix HWE displaying control analysis twice.
• Minor changes to vignette.
• Adjust Errors to only print out when Output=T.

BIGDAWG 1.3.6

• Added function to check Changes in version ersion and IMGT/HLA version simultaneously using CheckRelease().
• Removed UpdateRelease(GetRelease). See vignette.
• Vignette update to reflect changes.

BIGDAWG 1.3.5

• Minor wording change to vignette to enhance clarity and reflect GitHub availability.
• Added function to check release BIGDAWG uses for IMGT/HLA database. See vignette.
• Added Hardy Weinberg Equilibrium testing for cases. Useful when employing other binary phenotypes.
• Update bundled IMGT/HLA amino acid exon alignment to latest release (3.24.0)

BIGDAWG 1.3.4 (2016-04-10)

• Added output of subject haplotypes to file when running haplotype analysis.
• Bug fix in haplotype generation and outputs.
• Bug fix in when locus has only a single allele. Thanks go to Antoine Lizee.
• Other minor improvements to enhance data processing.
• Minor wording change to vignette to enhance clarity.
• Updated Human Immunology paper to BIGDAWG.
• 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.
• Added output of Sample IDs removed due to missing alleles exceeding set threshold.
• Adjusted Missing default to 2.
• When running multiple locus sets the for haplotype analysis, now displays which haplotype is being run.

BIGDAWG 1.2.8 (2016-02-29)

• Bug fix.

BIGDAWG 1.2.7

• Bug fix for chi square output using some data sets.

BIGDAWG 1.2.6 (2016-02-20)

• BIDAWG v1.2.1 - v1.2.5 unreleased internal versions.
• Bug fix when removing missing data as set by 'Missing' parameter. Thanks go to Arun Khattri.
• Added reference to BIGDAWG publication in DESCRIPTION and vignette.
• Update bundled IMGT/HLA amino acid exon alignment to latest release (3.23.0)

BIGDAWG 1.2.1 (2015-11-10)

• Added NEWS file to document BIGDAWG releases.
• Bug fix when EVS.rm was set to TRUE.
• Precheck.txt renamed to Data_Summary.txt.
• Distinction between Run parameters and Set parameters.
• Run Parameters generated and written to file earlier in script.
• Added section delimiter for 'Data Processing And Checks' in console output.
• Changes in wording for select BIGDAWG error messages.
• Update to Hardy-Weinberg test.
• Update bundled IMGT/HLA amino acid exon alignment to latest release (3.22.0)