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:
gaston_1.6.tar.gz
gaston_1.6.tar.gz(r-4.5-noble)gaston_1.6.tar.gz(r-4.4-noble)
gaston_1.6.tgz(r-4.4-emscripten)gaston_1.6.tgz(r-4.3-emscripten)
gaston.pdf |gaston.html✨
gaston/json (API)
NEWS
| # Install 'gaston' in R: |
| install.packages('gaston', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- AGT.bim - AGT data set
- AGT.fam - AGT data set
- AGT.gen - AGT data set
- AGT.pop - AGT data set
- LCT.bim - LCT data set
- LCT.fam - LCT data set
- LCT.gen - LCT data set
- LCT.pop - LCT data set
- TTN.bim - TTN data set
- TTN.fam - TTN data set
- TTN.gen - TTN data set
- TTN.pop - TTN data set
- dupli.bim - Small data set to illustrate 'SNP.rm.duplicates'
- dupli.gen - Small data set to illustrate 'SNP.rm.duplicates'
- dupli.ped - Small data set to illustrate 'SNP.rm.duplicates'
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 10 months agofrom:4db5af1055. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 03 2024 |
| R-4.5-linux-x86_64 | OK | Sep 03 2024 |
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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| gaston | gaston-package gaston |
| AGT data set | AGT AGT.bim AGT.fam AGT.gen AGT.pop |
| Creation of a bed.matrix | as.bed.matrix |
| Association Test | association.test |
| SNP loadings | bed.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 Matrix | DM |
| Small data set to illustrate 'SNP.rm.duplicates' | dupli dupli.bim dupli.gen dupli.ped dupli.pop |
| Genetic Relationship Matrix | GRM |
| Autosomes and X, Y, MT chromosomes | is.autosome is.chr.mt is.chr.x is.chr.y |
| LCT data set | LCT LCT.bim LCT.fam LCT.gen LCT.pop |
| Linkage Disequilibrium | LD |
| LD clumping | LD.clump |
| Plot Linkage Disequilibrium | LD.plot |
| LD thinning | LD.thin |
| Contour plot for two parameters likelihood | lik.contour |
| Linear mixed model fitting with AIREML | lmm.aireml |
| Linear mixed model fitting with the diagonalization trick | lmm.diago |
| Likelihood of a linear mixed model | lmm.diago.likelihood lmm.diago.profile.likelihood |
| Likelihood of a linear mixed model | lmm.profile.restricted.likelihood lmm.restricted.likelihood |
| Linear mixed model data simulation | lmm.simu |
| Logistic mixed model fitting with Penalized Quasi-Likelihood / AIREML | logistic.mm.aireml |
| Manhattan plot | manhattan |
| QQ plot of p-values | qqplot.pvalues |
| Random square definite positive matrix | random.pm |
| Read a 'bed.matrix' | read.bed.matrix |
| Create a 'bed.matrix' from VCF files | read.vcf |
| Reshape a Genetic Relationship Matrix | reshape.GRM |
| Score Test for Covariates with Fixed Effects in Linear or Logistic Mixed Model | score.fixed.linear score.fixed.logistic |
| Variance Component Test in Linear or Logistic Mixed Model | score.variance.linear score.variance.logistic |
| Subsetting from a 'bed.matrix' | select.inds |
| Subsetting from a 'bed.matrix' | select.snps |
| Set Genetic Distance | set.dist |
| Genomic Sex | set.genomic.sex |
| Hardy-Weinberg Equilibrium | set.hwe |
| Basic statistics for a 'bed.matrix' | set.stats set.stats.ped set.stats.snps |
| Duplicated SNPs | SNP.duplicated |
| SNP matching | SNP.match |
| Remove duplicated SNPs | SNP.rm.duplicates |
| Evaluation of a condition on SNPS or individuals in a 'bed.matrix' | test.inds test.snps which.inds which.snps |
| TTN data set | TTN TTN.bim TTN.fam TTN.gen TTN.pop |
| Save a 'bed.matrix' | write.bed.matrix |