NEWS

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SNPRelate 1.38.0

UTILITIES

• faster 'snpgdsLDpruning()' and new multi-threading implementation
• new option 'autosave' in 'snpgdsLDpruning()'
• new option 'start.pos="random.f500"' in 'snpgdsLDpruning()', allowing faster genotype scanning (it is used by default now). To be compatible with the previous versions, please specify 'start.pos="random"' manually
• Fix the welcome message when running in a non x86 system

SNPRelate 1.36.1

UTILITIES

• fix the compiler warning: -Wformat-security
• set 'maf=0.005' & 'missing.rate=0.05' by default in 'snpgdsLDpruning()' (for WGS data)
• show a progress bar in ‘snpgdsLDpruning()' when ’verbose=TRUE'
• update the help files of 'snpgdsAdmixProp()' and 'snpgdsAdmixPlot()'

SNPRelate 1.34.0

• fix the compiler warning: sprintf is deprecated

SNPRelate 1.32.0

• update the web links

SNPRelate 1.30.1

• return a object of S3 class "snpgdsGRMClass" in 'snpgdsGRM()' instead of a list when 'with.id=TRUE'
• fix a portable issue with Fortran character strings via USE_FC_LEN_T & FCONE

SNPRelate 1.24.0

• definition of IBS in the 'snpgdsIBS()' help file

SNPRelate 1.22.0

• 'allow.fork=TRUE' is the default in 'snpgdsOpen()' since v1.21.2
• add 'print.snpgdsPCAClass', 'print.snpgdsEigMixClass', 'print.snpgdsPCASNPLoadingClass', 'print, snpgdsEigMixSNPLoadingClass', 'print.snpgdsIBDClass', 'print.snpgdsDissClass', 'print.snpgdsIBSClass'
• fix a Win32 compiler issue with gcc-4.9
• update 'snpgdsBED2GDS()' with comment.char=""

SNPRelate 1.20.1

• Bug fix: eigenvalues and TraceXTX are correctly calculated in 'snpgdsPCA(, algorithm="randomized")'

SNPRelate 1.20.0

• a leading tilde in the file path is allowed in 'snpgdsGDS2BED()'
• change the file name "vignettes/SNPRelateTutorial.Rmd" to "vignettes/SNPRelate.Rmd", so 'vignette("SNPRelate")' can work directly

SNPRelate 1.18.1

• support long vector in 'snpgdsIBDSelection()'

SNPRelate 1.18.0

• 'snpgdsBED2GDS()' allows a single file name without the extended file names (.bed, .fam, .bim)

SNPRelate 1.16.0

• a new option 'useMatrix' for the packed symmetric matrix using the Matrix package in 'snpgdsIBDMoM()', 'snpgdsIBDKING()', 'snpgdsIBS()', 'snpgdsIndivBeta()' and 'snpgdsGRM()' to reduce memory usages
• fix a bug of missing sample and SNP IDs in the output of 'snpgdsIndInb()'
• new option 'start.pos' in 'snpgdsLDpruning()'
• new methods in 'snpgdsIndInb()': gcta1, gcta2, gcta3; progress information is shown during running the function
• 'snpgdsCombineGeno()' supports dosages

SNPRelate 1.14.0

• the default compression is "LZMA_RA" in 'snpgdsBED2GDS()', 'snpgdsVCF2GDS()' and 'snpgdsVCF2GDS_R()' for annotations
• support Intel C++ compiler with SSE2/AVX2
• allow interrupting requests in the calculation
• new method options in 'snpgdsPairScore()': GVH.major, GVH.minor, GVH.major.only, GVH.minor.only
• force to use integers for 'snp.position' in 'snpgdsCreateGeno()'
• unit tests for merging GRMs in 'snpgdsMergeGRM()'
• the function 'snpgdsSNPListStrand()' is merged to 'snpgdsSNPListIntersect()', and it is removed from the package
• update 'snpgdsSNPListIntersect()' and 'snpgdsCombineGeno()' (work correctly)
• replace INF/-INF by NaN in the output of 'snpgdsIBDKING()'

SNPRelate 1.12.0-1.12.2

• new arguments 'with.sample.id' and 'with.snp.id' in 'snpgdsSNPRateFreq()'
• fix an issue in the C code 'LENGTH or similar applied to NULL object'
• a new option 'method="Jacquard"' in 'snpgdsPairIBD()'
• 'snpgdsGRM()' can output the GRM matrix to a GDS file
• a new function 'snpgdsMergeGRM()' to merge multiple GRMs

SNPRelate 1.10.0-1.10.2

• new functions 'snpgdsAdmixPlot()' and 'snpgdsAdmixTable()'
• 'snpgdsPCASNPLoading()' and 'snpgdsPCASampLoading()' support the eigen results of 'snpgdsEIGMIX()' allowing projecting new samples to the existing coordinate
• 'snpgdsFst()' provides W&C84 mean Fst together with weighted Fst
• a new argument 'outgds' in 'snpgdsPCACorr()' allows exporting correlations to a gds file
• a friendly warning is given when openning a SeqArray file with 'snpgdsOpen()'
• a new option "Corr" in 'snpgdsGRM()' for scaled GRM
• progress information: showing overall running time when completed
• An unexpected exception in a thread could result in deadlock: the current implementation shows error information and exits the R session

SNPRelate 1.8.0

• add a new function 'snpgdsIndivBeta()'

SNPRelate 1.6.0-1.6.6

• fix an issue in 'snpgdsVCF2GDS()' if sample.id has white space
• bug fix in 'snpgdsPCASampLoading()' when the input is SeqArray GDS file
• improve 'snpgdsGetGeno()'
• the version number was bumped for the Bioconductor release version 3.3
• new implement of thread pool
• bitwise intrinsics (SSE2/AVX2) to accelerate 'snpgdsIBSNum()', 'snpgdsIBS()', 'snpgdsIBDMoM()', 'snpgdsIBDKing()' (+50% to +300%)
• v1.6.4: bug fix in v1.6.3 (allele counting error with SSE2 implement)
• v1.6.5: ‘snpgdsGRM()', renames the option "Visscher" to "GCTA", new option ’dosage' in 'snpgdsPairScore()', new function 'plot.snpgdsPCAClass()'

SNPRelate 1.4.0

• update GENEVA website address
• add a new function 'snpgdsPairScore()'
• improve 'snpgdsGRM()'
• support the SeqArray data format (requiring SeqArray >= v1.9.2)
• modification according to gdsfmt_1.5.7
• bug fix in 'snpgdsLDMat()' when genotype data are from SeqArray
• bug fix: https://github.com/zhengxwen/SNPRelate/issues/14
• 'snpgdsLDMat()' supports multiple threads and covariance
• ‘snpgdsPCA()': non-computed eigenvalues are NaN to avoid misuse of ’eigenval' when 'eigen.method="DSPEVX"'

SNPRelate 1.2.0

• fix a bug in ‘snpgdsVCF2GDS()' when ’method="biallelic.only"'
• add 'snpgdsVCF2GDS_R()' for the R implementation
• fix a bug in ‘snpgdsBED2GDS()' if ’family=TRUE'
• 'snpgdsGDS2BED()' allows the file name of GDS
• improve 'snpgdsSlidingWindow()'
• add an option 'ignore.chr.prefix' to the function 'snpgdsVCF2GDS()'
• a new function 'snpgdsHWE()'
• add "Fst estimation" to the vignette
• bug fix if 'requireNamespace("SNPRelate")' is called from other packages
• ‘snpgdsPCA()' uses ’DSPEVX' to compute eigenvalues and eigenvectors instead of 'DSPEV' if top eigenvalues are required only (significant improvement on computing speed)
• the original Rnw vignette is replaced by a R Markdown vignette
• a new function 'snpgdsPED2GDS()'

SNPRelate 1.0.0

• The version number was bumped for the Bioconductor release version

SNPRelate 0.99.1-0.99.3

• an option to create an integer snp.id when converting from PLINK
• a new function 'snpgdsFst()' to estimate Fst
• minor fixes

SNPRelate 0.99.0

• be a Bioconductor package
• fully support long vectors (>= R v3.0)
• >5x speedup in the function 'snpgdsVCF2GDS()'
• SNP GDS format allows character-type chromosome codes
• add a new argument 'ref.allele' in 'snpgdsVCF2GDS()'
• add new functions 'snpgdsOpen()' and 'snpgdsClose()'
• add a new function 'snpgdsTranspose()' to transpose the genotypic matrix
• add a new function 'snpgdsAlleleSwitch()' to switch alleles if needed
• add a new function 'snpgdsApartSelection()'
• add a new function 'snpgdsGEN2GDS()' to import Oxford GEN data
• use NA instead of 3 as missing value in 'snpgdsGetGeno()'
• add a new argument 'snpfirstdim' in the function 'snpgdsGDS2BED()'
• add a new argument 'with.id' in the functions 'snpgdsSNPRateFreq()' and 'snpgdsSampMissRate()'
• return a numeric vector instead of data.frame in 'snpgdsLDpair()'
• add estimating nine Jacquard's coefficients in 'snpgdsIBDMLE()'
• fix the memory issues reported by valgrind

SNPRelate 0.9.15-0.9.19

• improve 'snpgdsIBDKING()' to avoid misleading arguments and examples
• improve 'snpgdsIBDSelection()'
• the names of column 'sample1', 'sample2' and 'kinshipcoeff' are changed to 'ID1', 'ID2' and 'kinship' in the output of 'snpgdsIBDSelection()'
• avoid compiler issues when the version of R < v3.0
• minor fixes in 'snpgdsIBDSelection()': allow non-character-type sample IDs and missing IBD coefficients

SNPRelate 0.9.14 (2013-05-22)

• 'snpgdsGDS2BED()' gives a warning if the allele information is missing
• add 'snpgdsIBDKING()' (KING robust relationship inference in genome-wide association studies)
• bug fixes in 'snpgdsIBS()' and 'snpgdsIBSNum()'
• some warnings in 'snpgdsSummary()' are replaced by hints
• bug fix in 'snpgdsVCF2GDS()': duplicate SNP id when importing multiple VCF files
• improve hint information in 'snpgdsGDS2BED()'

SNPRelate 0.9.10-0.9.13

• disable parallel functions in the Windows version of SNPRelate, until the internal multi-thread funcitons are replaced by the functions in win-pthreads
• fix compiling issues in the Windows version of SNPRelate
• add 'GetRNGstate' and 'PutRNGstate' to the C function 'gnrDistPerm()'
• remove the upper limit of 200 chromosomes in 'snpgdsVCF2GDS()' according to scaffolds/contigs from a de novo assembly not chromosomes
• improve 'snpgdsSummary()'
• bug fixes in 'snpgdsPairIBD()'
• bug fix in 'snpgdsVCF2GDS()': to use "\t" as the field separator character
• bug fixes according to gdsfmt v0.9.11
• improve the vignette

SNPRelate 0.9.8-0.9.9

• adds a new argument 'family' to 'snpgdsBED2GDS()'
• improves 'snpgdsCutTree()'
• adds a new function 'snpgdsDrawTree()'
• adds an argument 'option' to the function 'snpgdsBED2GDS()'
• outputs chromosome codes according to 'snpgdsOption()' in 'snpgdsGDS2BED()'
• add an alternative method extracting variants from a VCF file in 'snpgdsVCF2GDS()'
• supports multiple files in 'snpgdsVCF2GDS()'
• add 'snpgdsOption()'
• add 'snpgdsHCluster()'
• add 'snpgdsCutTree()'
• add 'snpgdsDiss()'

SNPRelate 0.9.1-0.9.7

• bug fix: an important bug of missing genotypes in 'snpgdsVCF2GDS()'
• bug fix: a bug in 'snpgdsGDS2BED()' (output 23, 24, ..., instead of X, Y, XY)
• bug fix: a bug in 'snpgdsCombineGeno()' (due to duplicate SNPs)
• 'snpgdsLDpair()' provides haplotype frequency estimates
• 'snpgdsLDMat()' allows specifying sliding window size
• add RUnit tests
• add a vignette
• bug fixes
• add functions to 'snpgdsIBDMLE()' and 'snpgdsIBDMoM()'
• add a new function 'snpgdsVCF2GDS()'

SNPRelate 0.9.0 (2011-08-03)

• first public release of SNPRelate