Bioconductor Release v3.13

CHANGES IN VERSION 1.24.0

• definition of IBS in the snpgdsIBS help file

CHANGES IN VERSION 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=""

CHANGES IN VERSION 1.20.1

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

CHANGES IN VERSION 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

CHANGES IN VERSION 1.18.1

• support long vector in snpgdsIBDSelection()

Bioconductor Release v3.9

CHANGES IN VERSION 1.18.0

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

CHANGES IN VERSION 1.16.0

• a new option 'useMatrix' to allow 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

CHANGES IN VERSION 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 Bioconductor Release v3.6

The updates compared to v1.6.0:

New features:

• new arguments 'with.sample.id' and 'with.snp.id' in snpgdsSNPRateFreq()
• progress information: showing overall running time when completed
• 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 new option "Corr" in snpgdsGRM() for scaled GRM
• add a new function snpgdsIndivBeta()

Bug fixes

• fix an issue in C codes 'LENGTH or similar applied to NULL object'
• An unexpected exception in a thread could result in deadlock: the current implementation shows error information and exits the R session

Utilities

• a friendly warning is given when openning a SeqArray file with snpgdsOpen()

SNPRelate released together with SeqArray

v1.6.0

version bump

Bioconductor Release 3.2

1.4.0

BioC 3.2

Bioconductor Version

v0.99.0

Update README.md

Release

v0.9.20

Update README.md