NEWS.md

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

gaston 1.1

Corrections

• corrected C++ code (compilation errors on some distributions)

gaston 1.2

Improvements

• kinship matrix is now in single precision (faster)

• various minor changes

gaston 1.3

Bug fixes

• corrected bug in HWE chi square (monomorphic SNP)

New features

• select.snps and select.inds (negative indices, presence of NAs)

gaston 1.3.1

Bug fixes

• fixed an (intermittent) bug (?!) in kinhsip matrix computations

gaston 1.4

New features

• 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

Implementation details

• matrix4 now uses uint8_t array instead of char array (induced many small changes in the C++ code).

gaston 1.4.5

Bug fixes

• corrected a bug in method 'show'

Implementation details

• better handling of constraints in AIREML methods

• faster implementation of GRM

New features

• new function genomic.sex

gaston 1.4.6

Implementation details

• 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 features

• 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)

gaston 1.4.7

Bug fixes

• Corrected (minor) bug in association.test (handling of monomorphic SNPs in some tests)

New features

• 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)

gaston 1.4.8

Bug fixes

• Corrected bug in set.stats (stats for chr Y)

• Finally removed CompQuadForm from dependence list !

New features

• 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

gaston 1.4.9

New features

• 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

gaston 1.5

New features

• 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

gaston 1.5.1

New features

• 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

Implementation details

• Vignette in knitr

gaston 1.5.2

Implementation details

• Remove some compilation warnings (-Wreorder)

• Temporarily disable TBB (UBSAN test) + function setThreadOptions

gaston 1.5.3

Implementation details

• Cast in log() function (fix compilation error on solaris)

• Modified plot thinning in qqplot.pvalues

gaston 1.5.4

New features

• New functions SNP.rm.duplicates and set.dist

• Argument 'by = ' in SNP.match

Implementation details

• Re-enabled TBB

• Improved logistic regression code / small improvements in association.testa

gaston 1.5.5

Bug fixes

• Corrected naugthy bug in logistic regression (in case of 20 iterations, still compute covariance matrix!!!) (bug introduced in 1.5.4)

New features

• Started to write an FAQ

gaston 1.5.6

Bug fixes

• Corrected bug in gwas lmm wald (PQL) (was sending back NaNs only :/ )

gaston 1.5.7

Implementation details

• Corrected return; to return() as requested by the CRAN

• Improved code for snp_hash.h (from gaston.utils)

New features

• Argument EM in logistic-mm-aireml

gaston 1.5.8

New features

• new function LD.clump

gaston 1.5.9

New features

• Default argument max.dist = 500e3 in LD.thin

Bug fixes

• Corrected bug in ld clump, thanks to valgrind and Pr Ripley <3

gaston 1.6

Bug fixes

• Corrected (minor) bugs in manhattan plot / qqplot functions

gaston documentation built on May 29, 2024, 7:33 a.m.