NEWS

---

pould 1.0.1 (2020-10-16)

• 2020-10-08
• Resubmitted for unarchiving from CRAN.

pould 1.0.0 (2020-04-15)

• 2020-04-10
• Included options for users to specify the directory into which files should be written for cALD(), LD.heat.map(), LD.sign.test() and LDwrap().
• Changed cat() messages to warning messages() in LD.heat.map(), LD.sign.test() and LDWrap().
• Renamed the reportVector parameter in cALD to saveVector.
• Submission to CRAN.

pould 0.10.5.9000

• 2020-02-21
• Changes to documentation in advance of CRAN submission.

pould 0.10.4.9000

• 2019-10-17
• Updated the vignette to include recommendations on locus order.

pould 0.10.3.9000

• 2019-10-15
• Updated LDWrap() and parseGenotypes() to to streamline parsing and processing of 'untyped data'.

pould 0.10.2.9000

• 2019-10-14
• Updated LDWrap() and parseGenotypes() to reject single-locus genotype files.
• Additional updates to LDWrap() to support text files.

pould 0.10.1.9000

• 2019-10-08
• Updated LDWrap() to accomodate tab-delimited text (.txt or .tsv) format files.

pould 0.10.0.9000

• 2019-10-05
• Updated package DESCRIPTION.
• Updated LD.heat.map() to account for locus pairs with no LD values.
• Added the parseGenotypes() function to support column-formatted genotype data.
• Updated LDWrap() to incorporate parseGenotypes().
• Updated the citations to reflect recent publications.
• Updated the Vignette.

pould 0.9.1.9000

• Removed notes regarding gap::LDkl() from ReadMe and Vignette documents.
• Updated documentation for LDWrap() to reflect current data requirements.

pould 0.9.0.9000

• Added the trimAlleles() function to LDWrap() to enable the truncation of colon-delimited allele names to a specified number of fields.
• When a positive trunc value is provided to LDWrap(), the generated files include the truncation level in their filenames.
• Updated the documentation for cALD()'s vectorPrefix parameter.
• Updated the ReadMe.md and Vignette documents to reflect these changes.
• Thanks to K. Osoegawa for suggesting the above improvements.
• Added a user notification to LDWrap() for instances when famData is not defined.
• Corrected a typo in the LD.heat.map documentation.
• Reformatted NEWS to function under R version 3.6.0.
• Updated DESCRIPTION file.

pould 0.8.5.9000

• Addressed a Warning being generated by LD.heat.map().
• Shortened an example on the LD.heat.map() Help Page.
• Updated the message delivered by LD.heat.map() when different loci are included in specified phased and unphased LDWrap() outputs.

pould 0.8.4.9000

• Added the phasedData and unphasedData parameters to LD.heat.map(), allowing users to identifify specific LDWrap() output files to be used to generate heatmaps.
• Modified the LD.heat.map() Vignette and function documentation to reflect these changes.
• Modified the 6-21-2019 NEWS entry for grammar and accuracy.

pould 0.8.3.9000

• Corrected the citation for the publication describing this package in the LD.heat.map(), LD.sign.test() and LDWrap() functions.
• Expanded the package name in the GitHub ReadMe document.
• Added the note about the LDkl() function in the gap package to the ReadMe and moved this note higher in the vignette.

pould 0.8.2.9000

• Added phasedLabel and unphasedLabel to LD.heat.map(), allowing users to specify the labels associated with the upper and lower half of each plot.
• Modified the LD.heat.map() Vignette and function documentation to reflect these changes, and to cite a publication describing this package.
• Happy Summer Solstice!

pould 0.8.1.9000

• Added the color parameter to LD.heat.map(), allowing color or grey-scale heat-map plots to be generated.
• Added the color parameter to the Vignette and LD.heat.map() documentation.
• Added keywords to the LD.heat.map() documentation.
• Modified the LDWrap() Vignette to make it clear that ambiguous allele and genotype data cannot be included in LDWrap() data files.
• Removed example non-ggplot heat-map code.

pould 0.8.0.9000

• Added the LD.heat.map() function to generate heat maps of LD values from the LD data exported from LDWrap().
• Updated the ReadMe.md and Vignette documents to reflect the changes to LDWrap() and the addition of the LD.heat.map() function.

pould 0.7.0.9000

• Added a Reference to the documentation of LDWrap() and LD.sign.test().
• Added the extractLoci() function to LDWrap() to automate the processing of locus information from haplotype datasets, accommodating non-HLA data.

pould 0.6.3.9000

• Modified Vignette to reflect the limitations of LDkl in the gap package and the availability of an updated gap package on GitHub.
• Modified ReadMe.md document to include devtools installation instructions.
• Thanks to L. Creary for identifying both issues.
• Modified Description to mention sign tests.

pould 0.6.2.9000

• Modified cALD(), LDWrap() and LD.sign.test() so that output files are always written to the working directory.

pould 0.6.1.9000

• Updated LDWrap() documentation to include caveats regarding the analysis of unusual and truncated allele names.
• Added package versioning to the README.md document.

pould 0.6.0.9000

• Added the LD.sign.test() function.
• Updated documentation to reflect this addition.
• Corrected a typo in 5-18-2018 News entry.

pould 0.5.0.9000

• Modified LDWrap() to avoid calling cALD() for locus pairs in which at least one locus is monomorphic. In these cases, the *LD_results.csv file identifies which loci were monomorphic for that locus pair.
• Updated documentation to reflect this.

pould 0.4.2.9000

• Streamlined the integration of cALD() into LDWrap().

pould 0.4.1.9000

• Updated the Vignette and ReadMe file to correct versioning, punctuation and spelling errors, and elaborate on documentation for cALD()'s report of the number of haplotypes.

pould 0.4.0.9000

• Added the number of haplotypes evaluated to the values returned by cALD(), and thereby to the content of the *LD_results.csv file generated by LDWrap().
• Updated the documentation to reflect this.

pould 0.3.0.9000

• Revised drb1.dqb1.demo so that it represents phased DRB1~DQB1 data pulled directly from hla.hap.demo.
• Added README.Rmd and README.md files for GitHub.
• Added NEWS.
• Added Vignette.
• Changed LDWrap() notification for input data lacking required columns, to reflect the data source as either a data frame or a file.
• Removed the passFile parameter from cALD(), and updated documentation.

pould 0.2.1.9000

• Added dataset documentation files.

pould 0.2.0.9000

• Added *Rd files for each function.
• Added hla.hap.demo and drb1.dqb1.demo datasets.

pould 0.1.0.9000

• Created package that includes the exported LDWrap() and cALD() functions, and the internal writeVector() function.