Package: gaston 1.6

Hervé Perdry

gaston: 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 <doi:10.1159/000488519>.

Authors:Hervé Perdry [cre, aut, cph], Claire Dandine-Roulland [aut, cph], Deepak Bandyopadhyay [cph], Lutz Kettner [cph]

gaston_1.6.tar.gz
gaston_1.6.tar.gz(r-4.7-arm64)gaston_1.6.tar.gz(r-4.7-x86_64)gaston_1.6.tar.gz(r-4.6-arm64)gaston_1.6.tar.gz(r-4.6-x86_64)
gaston_1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gaston/json (API)

# Install 'gaston' in R:
install.packages('gaston', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

zlibcpp

7.62 score 6 stars 12 packages 246 scripts 6.6k downloads 6 mentions 60 exports 3 dependencies

Last updated from:4db5af1055. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK352
linux-devel-x86_64OK371
source / vignettesOK577
linux-release-arm64OK372
linux-release-x86_64OK368
wasm-releaseOK369

Exports:as.bed.matrixas.matrixassociation.testbed.loadingscbindDMGRMheadis.autosomeis.chr.mtis.chr.xis.chr.yLDLD.clumpLD.plotLD.thinlik.contourlmm.airemllmm.diagolmm.diago.likelihoodlmm.diago.profile.likelihoodlmm.profile.restricted.likelihoodlmm.restricted.likelihoodlmm.simulogistic.mm.airemlmanhattanmumu<-pp<-qqplot.pvaluesrandom.pmrbindread.bed.matrixread.vcfreshape.GRMscore.fixed.linearscore.fixed.logisticscore.variance.linearscore.variance.logisticselect.indsselect.snpsset.distset.genomic.sexset.hweset.statsset.stats.pedset.stats.snpssigmasigma<-SNP.duplicatedSNP.matchSNP.rm.duplicatesstandardizestandardize<-test.indstest.snpswhich.indswhich.snpswrite.bed.matrix

Dependencies:RcppRcppEigenRcppParallel

gaston faq
Rendered fromgaston-faq.Rnwusingknitr::knitr

Last update: 2023-12-08
Started: 2019-04-02

gaston package
Rendered fromgaston.Rnwusingknitr::knitr

Last update: 2019-04-02
Started: 2015-10-02

Readme and manuals

Help Manual

Help pageTopics
gastongaston-package gaston
AGT data setAGT AGT.bim AGT.fam AGT.gen AGT.pop
Creation of a bed.matrixas.bed.matrix
Association Testassociation.test
SNP loadingsbed.loadings
Class '"bed.matrix"'%*%,bed.matrix,matrix-method %*%,bed.matrix,vector-method %*%,matrix,bed.matrix-method %*%,vector,bed.matrix-method as.matrix,bed.matrix-method bed.matrix bed.matrix-class cbind cbind,bed.matrix-method coerce,bed.matrix,matrix-method coerce,bed.matrix,vector-method coerce,matrix,bed.matrix-method coerce,vector,bed.matrix-method dim,bed.matrix-method head,bed.matrix-method matrix,data.frameOrNULL,data.frameOrNULL-method mu mu,bed.matrix-method mu<- mu<-,bed.matrix-method p p,bed.matrix-method p<- p<-,bed.matrix-method rbind rbind,bed.matrix-method show,bed.matrix-method sigma sigma,bed.matrix-method sigma<- sigma<-,bed.matrix-method standardize standardize,bed.matrix-method standardize<- standardize<-,bed.matrix-method [,bed.matrix,logical,logical,missing-method [,bed.matrix,logical,missing,missing-method [,bed.matrix,logical,numeric,missing-method [,bed.matrix,missing,logical,missing-method [,bed.matrix,missing,numeric,missing-method [,bed.matrix,numeric,logical,missing-method [,bed.matrix,numeric,missing,missing-method [,bed.matrix,numeric,numeric,missing-method
Dominance MatrixDM
Small data set to illustrate 'SNP.rm.duplicates'dupli dupli.bim dupli.gen dupli.ped dupli.pop
Genetic Relationship MatrixGRM
Autosomes and X, Y, MT chromosomesis.autosome is.chr.mt is.chr.x is.chr.y
LCT data setLCT LCT.bim LCT.fam LCT.gen LCT.pop
Linkage DisequilibriumLD
LD clumpingLD.clump
Plot Linkage DisequilibriumLD.plot
LD thinningLD.thin
Contour plot for two parameters likelihoodlik.contour
Linear mixed model fitting with AIREMLlmm.aireml
Linear mixed model fitting with the diagonalization tricklmm.diago
Likelihood of a linear mixed modellmm.diago.likelihood lmm.diago.profile.likelihood
Likelihood of a linear mixed modellmm.profile.restricted.likelihood lmm.restricted.likelihood
Linear mixed model data simulationlmm.simu
Logistic mixed model fitting with Penalized Quasi-Likelihood / AIREMLlogistic.mm.aireml
Manhattan plotmanhattan
QQ plot of p-valuesqqplot.pvalues
Random square definite positive matrixrandom.pm
Read a 'bed.matrix'read.bed.matrix
Create a 'bed.matrix' from VCF filesread.vcf
Reshape a Genetic Relationship Matrixreshape.GRM
Score Test for Covariates with Fixed Effects in Linear or Logistic Mixed Modelscore.fixed.linear score.fixed.logistic
Variance Component Test in Linear or Logistic Mixed Modelscore.variance.linear score.variance.logistic
Subsetting from a 'bed.matrix'select.inds
Subsetting from a 'bed.matrix'select.snps
Set Genetic Distanceset.dist
Genomic Sexset.genomic.sex
Hardy-Weinberg Equilibriumset.hwe
Basic statistics for a 'bed.matrix'set.stats set.stats.ped set.stats.snps
Duplicated SNPsSNP.duplicated
SNP matchingSNP.match
Remove duplicated SNPsSNP.rm.duplicates
Evaluation of a condition on SNPS or individuals in a 'bed.matrix'test.inds test.snps which.inds which.snps
TTN data setTTN TTN.bim TTN.fam TTN.gen TTN.pop
Save a 'bed.matrix'write.bed.matrix