CHANGES IN VERSION 1.16.0 ------------------------- o KIR information in `hlaLociInfo()` o new functions `hlaGenoSubsetFlank()` and `hlaLDMatrix()` CHANGES IN VERSION 1.14.0 ------------------------- o modify the kernel to support the GPU extension o add matching proportion to measure the similarity of SNP haplotypes between training and test datasets o new function `hlaReportPlot()` o the argument 'cl' in `predict.hlaAttrBagClass()`, `hlaPredict()` and `hlaParallelAttrBagging()` allows a numeric value for the number of cores CHANGES IN VERSION 1.12.0 ------------------------- o change "hg20" to "hg38" according to the UCSC Genome Browser datasets and documentation o add "DRB3" and "DRB4" to the HLA gene list CHANGES IN VERSION 1.10.0 ------------------------- o the version number was bumped for the Bioconductor release version 3.4 CHANGES IN VERSION 1.9.0-1.9.3 ------------------------- o the development version CHANGES IN VERSION 1.8.0-1.8.3 ------------------------- o the version number was bumped for the Bioconductor release version 3.3 o new arguments 'pos.start' and 'pos.end' in `hlaFlankingSNP()` CHANGES IN VERSION 1.7.0-1.7.7 ------------------------- o new functions `hlaCheckAllele()`, `hlaAssocTest()`, `hlaConvSequence()` and `summary.hlaAASeqClass()` CHANGES IN VERSION 1.6.0 ------------------------- o the version number was bumped for the Bioconductor release version 3.2 CHANGES IN VERSION 1.5.0-1.5.1 ------------------------- o increase the test coverage o fix an issue when `predict.hlaAttrBagClass(..., allele.check=FALSE)` CHANGES IN VERSION 1.4.0 ------------------------- o the version number was bumped for the Bioconductor release version 3.1 CHANGES IN VERSION 1.3.0-1.3.2 ------------------------- NEW FEATURES o support the human genome "hg20"/"hg38" o add a new function `hlaGDS2Geno()` to support SNP GDS files (in the R/Bioconductor package SNPRelate) o `hlaReport()` outputs text with markdown format SIGNIFICANT USER-VISIBLE CHANGES o optimize the calculation of hamming distance using SSE2 and hardware POPCNT instructions if available o hardware POPCNT: 2.4x speedup for large-scale data, compared to the implementation in v1.2.4 o SSE2 popcount implementation: 1.5x speedup for large-scale data, compared to the implementation in v1.2.4 BUG FIXES o bug fixes on big-endian machines (like Solaris SPARC, Apple PowerPC) o minor fix on random sampling from discrete uniform distribution o bug fix if `requireNamespace("HIBAG")` instead of `require(HIBAG)` is called from other packages CHANGES IN VERSION 1.2.1-1.2.4 ------------------------- NEW FEATURES o add a new function `hlaOutOfBag()` offering out-of-bag estimation of overall accuracy, per-allele sensitivity, etc o improve the display of the function `hlaReport()` SIGNIFICANT USER-VISIBLE CHANGES o improve the display of `summary.hlaAlleleClass()` o fix warnings in 'R-3.1.1 CMD check' o avoid missing values in `hlaFlankingSNP()` o add more gene information in `hlaLociInfo()` BUG FIXES o make the C function 'HIBAG_SortAlleleStr' compatible with the clang++ compiler on Mac Mavericks CHANGES IN VERSION 1.2.0 ------------------------- NEW FEATURES o add a new function `hlaPredMerge()` to merge predictions from multiple models via voting o add assembly information (like hg19) to the objects of 'hlaAttrBagClass' and 'hlaAttrBagObj' o add a new argument 'stop.cluster' to `hlaParallelAttrBagging()` o allow matching SNPs by positions only o allow imputing HLA alleles in parallel at a single locus SIGNIFICANT USER-VISIBLE CHANGES o optimize the C code: replace some intensive 'exp' and 'log' calculations by precalculated values, roughly 2.5x ~ 4x speedup o optimize the C code of the hamming distance calculation between genotypes and two haplotypes by SSE2 intrinsics, ~50% faster for large datasets o the code optimization guarantees the same training and predictive accuracies as version 1.1.0 o remove unused row names in the function `hlaCompareAllele()` o improve the function `hlaPublish()` o improve vignettes and documents CHANGES IN VERSION 1.1.0 ------------------------- NEW FEATURES o add genome assembly information (such like hg18, hg19) o allow class majority voting in `predict.hlaAttrBagClass()` o add an autosave function to `hlaParallelAttrBagging()` o add a new function `hlaPublish()` o allow additional information in the objects of 'hlaAttrBagClass' and 'hlaAttrBagObj' SIGNIFICANT USER-VISIBLE CHANGES o update citation information o change `hlaModelfromObj()` to `hlaModelFromObj()` (a typo) o improvement in mismatching alleles for allelic strands CHANGES IN VERSION 1.0.0 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o increase the limit of the possible number of SNPs in a single classifier up to 256 BUG FIXES o use `useDynLib()` in NAMESPACE instead of 'library.dynam()' since R-Ext strongly suggests to use `useDynLib()` o update citation information o add a vignette CHANGES IN VERSION 0.9.2-0.9.4 ------------------------- NEW FEATURES o add a load balancing function to `hlaParallelAttrBagging()` o add `hlaUniqueAllele()` o add an argument 'match.pos' to the functions `predict.hlaAttrBagClass()`, `hlaGenoCombine()`, `hlaGenoSwitchStrand()` o add an argument 'with.pos' to the function `hlaSNPID()` SIGNIFICANT USER-VISIBLE CHANGES o give more warnings about missing SNPs in `predict.hlaAttrBagClass()` o a warning is given for strand mismatching when calling `hlaGenoSwitchStrand()` BUG FIXES o bug fix: passing only one individual to `predict.hlaAttrBagClass()` o avoid the segmentation fault in `predict.hlaAttrBagClass()` when all SNPs are missing. CHANGES IN VERSION 0.9.1 ------------------------- o first release of HIBAG in July, 2012