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NEWS
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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