Man pages for gaston
Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

AGTAGT data set
as.bed.matrixCreation of a bed.matrix
association.testAssociation Test
bed.loadingsSNP loadings
bed.matrix-classClass '"bed.matrix"'
DMDominance Matrix
dupliSmall data set to illustrate 'SNP.rm.duplicates'
gaston-packagegaston
GRMGenetic Relationship Matrix
is.autosomeAutosomes and X, Y, MT chromosomes
LCTLCT data set
LDLinkage Disequilibrium
LD.plotPlot Linkage Disequilibrium
LD.thinLD thinning
lik.contourContour plot for two parameters likelihood
lmm.airemlLinear mixed model fitting with AIREML
lmm.diagoLinear mixed model fitting with the diagonalization trick
lmm.diago.likelihoodLikelihood of a linear mixed model
lmm.restricted.likelihoodLikelihood of a linear mixed model
lmm.simuLinear mixed model data simulation
logistic.mm.airemlLogistic mixed model fitting with Penalized Quasi-Likelihood...
manhattanManhattan plot
qqplot.pvaluesQQ plot of p-values
random.pmRandom square definite positive matrix
read.bed.matrixRead a 'bed.matrix'
read.vcfCreate a 'bed.matrix' from VCF files
reshape.GRMReshape a Genetic Relationship Matrix
score.fixedScore Test for Covariates with Fixed Effects in Linear or...
score.varianceVariance Component Test in Linear or Logistic Mixed Model
select.indsSubsetting from a 'bed.matrix'
select.snpsSubsetting from a 'bed.matrix'
set.distSet Genetic Distance
set.genomic.sexGenomic Sex
set.hweHardy-Weinberg Equilibrium
set.statsBasic statistics for a 'bed.matrix'
SNP.duplicatedDuplicated SNPs
SNP.matchSNP matching
SNP.rm.duplicatesRemove duplicated SNPs
TestsEvaluation of a condition on SNPS or individuals in a...
TTNTTN data set
write.bed.matrixSave a 'bed.matrix'
gaston documentation built on July 16, 2018, 1:02 a.m.