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

Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al .


1.1: corrected C++ code (compilation errors on some distributions) 1.2: kinhsip matrix is now in single precision (faster) various minor changes 1.3: corrected bug in HWE chi square (monomorphic SNP) select.snps and select.inds (negative indices, presence of NAs) 1.3.1: suppressed various attribute ((aligned(16))) in m4_kinship*.cpp which seemed to be causing an (intermittent) bug (?!) 1.4: introduced option / updated vignette accordingly +hz in ped stats new function reshape.GRM as.bed.matrix no longer is a method, but a function minor modifs in read.vcf matrix4 now uses uint8_t array instead of char array (induced many small changes in the C++ code). 1.4.5: corrected a bug in method 'show' better handling of constraints in AIREML methods faster implementation of GRM new function 1.4.6: 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, 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) 1.4.7: Corrected (minor) bug in association.test (handling of monomorphic SNPs in some tests) New function LD.plot / LDheatmap dependence removed Handling NAs in select.snp select.inds Added chr X, Y, MT support / modified set.stats, 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 (CompQuadForm does not compile with R < 3.3 which bothers us) Minor modifications of the vignette (update description of modified functions) 1.4.8: Corrected bug in set.stats (stats for chr Y) Finally removed CompQuadForm from dependence list ! Minor modifs in read vcf, rbind, New function merge.inds (finalement, pas exportée) New functions (short cuts) is.autosome, is.chr.x, is.chr.y, 1.4.9: 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 1.5: 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 1.5.1: Improved functions association.test / Vignette in knitr 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 1.5.2 Remove some compilation warnings (-Wreorder) Temporarily disable TBB (UBSAN test) + function setThreadOptions 1.5.3 Cast in log() function (fix compilation error on solaris) Modified plot thinning in qqplot.pvalues 1.5.4 New functions SNP.rm.duplicates and set.dist Argument 'by = ' in SNP.match Re-enabled TBB Improved logistic regression code / small improvements in association.test

Reference manual

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1.5.5 by Hervé Perdry, 2 months ago

Browse source code at

Authors: Hervé Perdry [cre, aut, cph] , Claire Dandine-Roulland [aut, cph] , Deepak Bandyopadhyay [cph] (C++ gzstream class) , Lutz Kettner [cph] (C++ gzstream class)

Documentation:   PDF Manual  

GPL-3 license

Depends on Rcpp, RcppParallel, methods

Suggests knitr

Linking to Rcpp, RcppParallel, RcppEigen

See at CRAN