High-Performance Open-Source Archive
kinship matrix is now in single precision (faster)
various minor changes
introduced option gastion.auto.set.stats / updated vignette accordingly
added ‘hz’ in ped stats
new function reshape.GRM
as.bed.matrix no longer is a method, but a function
minor modifs in read.vcf
uint8_t array instead of char array
(induced many small changes in the C++ code).better handling of constraints in AIREML methods
faster implementation of GRM
Modified Imports/Depends fields to remove a warning about RcppParallel
Modified VCF handling functions to follow the new interface of WhopGenome (patch by Tomas Kalibera and Ulrich Wittelsbuerger)
New functions logistic.mm.aireml, score.variance.linear, score.variance.logistic, score.fixed.linear, score.fixed.logistic
New argument get.P in lmm.aireml
New features and arguments in association.test
Minor modifications of the vignette (illustration of association.test)
New function LD.plot (LDheatmap dependence removed)
Handling NAs in select.snp select.inds
Added chr X, Y, MT support / modified set.stats, set.genomic.sex accordingly
Added which.snps argument in LD.thin and GRM
rbind and cbind now check individuals ids / snp ids ; rbind check reference alleles and perform reference inversions / strand flips if needed.
Integrated code from CompQuadForm / removed dependence
Minor modifications of the vignette (update description of modified functions)
Corrected bug in set.stats (stats for chr Y)
Finally removed CompQuadForm from dependence list !
Minor modifs in read vcf, rbind, set.genomic.sex
New function merge.inds (function finally not exported)
New functions (short cuts) is.autosome, is.chr.x, is.chr.y, is.chr.mt
Modification of rbind, cbind to handle bed.matrices with different column names in @ped, @snps
A new test in association.test
Minor changes in GRM and LD.thin
VCF files support
Computation of the Dominance Matrix (DM)
New functions test.snps test.inds which.snps which.inds
Faster optimization with the diagonalization trick
Auto set the #threads when loaded
Improved functions association.test / random.pm
cbind : now keep p, mu, sigma
rbind : now handles alleles longer than 1
New functions qqplot.pvalue, manhattan
New functions SNP.duplicated, SNP.match
New functions lmm.restricted.likelihood, lmm.profile.restricted.likelihood
Remove some compilation warnings (-Wreorder)
Temporarily disable TBB (UBSAN test) + function setThreadOptions
Cast in log() function (fix compilation error on solaris)
Modified plot thinning in qqplot.pvalues
New functions SNP.rm.duplicates and set.dist
Argument ‘by =’ in SNP.match
Re-enabled TBB
Improved logistic regression code / small improvements in association.testa
Corrected return; to return() as requested by the CRAN
Improved code for snp_hash.h (from gaston.utils)
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