Releases · zhengxwen/SNPRelate

11 Jun 06:13

CHANGES IN VERSION 1.24.0

'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=""

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

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

Assets 2

07 May 20:15

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

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

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()

Assets 2

05 Dec 02:20

The updates compared to v1.6.0:

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()

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