CHANGES IN VERSION 1.1.0-1.1.11 ------------------------- o fix a bug in snpgdsVCF2GDS when 'method="biallelic.only"' o add 'snpgdsVCF2GDS_R' for the R implementation o fix a bug in 'snpgdsBED2GDS' if 'family=TRUE' o 'snpgdsGDS2BED' allows the file name of GDS o improve 'snpgdsSlidingWindow' o add an option 'ignore.chr.prefix' to the function 'snpgdsVCF2GDS' o a new function 'snpgdsHWE' o v1.1.5: add 'Fst estimation' to the vignette o v1.1.6: bug fix if 'requireNamespace("SNPRelate")' is called from other packages o v1.1.7: snpgdsPCA uses 'DSPEVX' to compute eigenvalues and eigenvectors instead of 'DSPEV' if top eigenvalues are required only (significant improvement on computing speed) o v1.1.8: the original Rnw vignette is replaced by a R Markdown vignette o v1.1.9: a new function 'snpgdsPED2GDS' CHANGES IN VERSION 1.0.0 ------------------------- o The version number was bumped for the Bioconductor release version CHANGES IN VERSION 0.99.1-0.99.3 ------------------------- o an option to create an integer snp.id when converting from PLINK o a new function 'snpgdsFst' to estimate Fst o minor fixes CHANGES IN VERSION 0.99.0 ------------------------- o be a Bioconductor package o fully support long vectors (>= R v3.0) o >5x speedup in the function 'snpgdsVCF2GDS' o SNP GDS format allows character-type chromosome codes o add a new argument 'ref.allele' in 'snpgdsVCF2GDS' o add new functions 'snpgdsOpen' and 'snpgdsClose' o add a new function 'snpgdsTranspose' to transpose the genotypic matrix o add a new function 'snpgdsAlleleSwitch' to switch alleles if needed o add a new function 'snpgdsApartSelection' o add a new function 'snpgdsGEN2GDS' to import Oxford GEN data o use NA instead of 3 as missing value in 'snpgdsGetGeno' o add a new argument 'snpfirstdim' in the function 'snpgdsGDS2BED' o add a new argument 'with.id' in the functions 'snpgdsSNPRateFreq' and 'snpgdsSampMissRate' o return a numeric vector instead of data.frame in 'snpgdsLDpair' o add estimating nine Jacquard's coefficients in 'snpgdsIBDMLE' o fix the memory issues reported by valgrind CHANGES IN VERSION 0.9.15-0.9.19 ------------------------- o improve 'snpgdsIBDKING' to avoid misleading arguments and examples o improve 'snpgdsIBDSelection' o the names of column 'sample1', 'sample2' and 'kinshipcoeff' are changed to 'ID1', 'ID2' and 'kinship' in the output of 'snpgdsIBDSelection' o avoid compiler issues when the version of R < v3.0 o minor fixes in 'snpgdsIBDSelection': allow non-character-type sample IDs and missing IBD coefficients CHANGES IN VERSION 0.9.14: ------------------------- o 'snpgdsGDS2BED' gives a warning if the allele information is missing o add 'snpgdsIBDKING' (KING robust relationship inference in genome-wide association studies) o bug fixes in 'snpgdsIBS' and 'snpgdsIBSNum' o some warnings in 'snpgdsSummary' are replaced by hints o bug fix in 'snpgdsVCF2GDS': duplicate SNP id when importing multiple VCF files o improve hint information in 'snpgdsGDS2BED' CHANGES IN VERSION 0.9.10-0.9.13 ------------------------- o disable parallel functions in the Windows version of SNPRelate, until the internal multi-thread funcitons are replaced by the functions in win-pthreads o fix compiling issues in the Windows version of SNPRelate o add 'GetRNGstate' and 'PutRNGstate' to the C function 'gnrDistPerm' o remove the upper limit of 200 chromosomes in 'snpgdsVCF2GDS' according to scaffolds/contigs from a de novo assembly not chromosomes o improve 'snpgdsSummary' o bug fixes in 'snpgdsPairIBD' o bug fix in 'snpgdsVCF2GDS': to use "\t" as the field separator character o bug fixes according to gdsfmt v0.9.11 o improve the vignette CHANGES IN VERSION 0.9.8-0.9.9 ------------------------- o adds a new argument 'family' to 'snpgdsBED2GDS' o improves 'snpgdsCutTree' o adds a new function 'snpgdsDrawTree' o adds an argument 'option' to the function 'snpgdsBED2GDS' o outputs chromosome codes according to 'snpgdsOption' in 'snpgdsGDS2BED' o add an alternative method extracting variants from a VCF file in 'snpgdsVCF2GDS' o supports multiple files in 'snpgdsVCF2GDS' o add 'snpgdsOption' o add 'snpgdsHCluster' o add 'snpgdsCutTree' o add 'snpgdsDiss' CHANGES IN VERSION 0.9.1-0.9.7 ------------------------- o bug fix: an important bug of missing genotypes in 'snpgdsVCF2GDS' o bug fix: a bug in 'snpgdsGDS2BED' (output 23, 24, ..., instead of X, Y, XY) o bug fix: a bug in 'snpgdsCombineGeno' (due to duplicate SNPs) o 'snpgdsLDpair' provides haplotype frequency estimates o 'snpgdsLDMat' allows specifying sliding window size o add RUnit tests o add a vignette o bug fixes o add functions to 'snpgdsIBDMLE' and 'snpgdsIBDMoM' o add a new function 'snpgdsVCF2GDS' CHANGES IN VERSION 0.9.0 (03-Aug-2011) ------------------------- o first public release of SNPRelate