Release Bioconductor Release v3.9 · zhengxwen/SNPRelate

CHANGES IN VERSION 1.18.0

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()