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

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Documentation for package ‘gaston’ version 1.5.9

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gaston-package gaston
%*%-method Class '"bed.matrix"'
AGT AGT data set
AGT.bim AGT data set
AGT.fam AGT data set
AGT.gen AGT data set
AGT.pop AGT data set
as.bed.matrix Creation of a bed.matrix
as.matrix-method Class '"bed.matrix"'
association.test Association Test
bed.loadings SNP loadings
bed.matrix Class '"bed.matrix"'
bed.matrix-class Class '"bed.matrix"'
cbind Class '"bed.matrix"'
cbind-method Class '"bed.matrix"'
coerce-method Class '"bed.matrix"'
dim-method Class '"bed.matrix"'
DM Dominance Matrix
dupli Small data set to illustrate 'SNP.rm.duplicates'
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'
dupli.pop Small data set to illustrate 'SNP.rm.duplicates'
gaston gaston
GRM Genetic Relationship Matrix
head-method Class '"bed.matrix"'
is.autosome Autosomes and X, Y, MT chromosomes
is.chr.mt Autosomes and X, Y, MT chromosomes
is.chr.x Autosomes and X, Y, MT chromosomes
is.chr.y Autosomes and X, Y, MT chromosomes
LCT LCT data set
LCT.bim LCT data set
LCT.fam LCT data set
LCT.gen LCT data set
LCT.pop LCT data set
LD Linkage Disequilibrium
LD.clump LD clumping
LD.plot Plot Linkage Disequilibrium
LD.thin LD thinning
lik.contour Contour plot for two parameters likelihood
lmm.aireml Linear mixed model fitting with AIREML
lmm.diago Linear mixed model fitting with the diagonalization trick
lmm.diago.likelihood Likelihood of a linear mixed model
lmm.diago.profile.likelihood Likelihood of a linear mixed model
lmm.profile.restricted.likelihood Likelihood of a linear mixed model
lmm.restricted.likelihood Likelihood of a linear mixed model
lmm.simu Linear mixed model data simulation
logistic.mm.aireml Logistic mixed model fitting with Penalized Quasi-Likelihood / AIREML
manhattan Manhattan plot
matrix-method Class '"bed.matrix"'
mu Class '"bed.matrix"'
mu-method Class '"bed.matrix"'
mu<- Class '"bed.matrix"'
mu<--method Class '"bed.matrix"'
p Class '"bed.matrix"'
p-method Class '"bed.matrix"'
p<- Class '"bed.matrix"'
p<--method Class '"bed.matrix"'
qqplot.pvalues QQ plot of p-values
random.pm Random square definite positive matrix
rbind Class '"bed.matrix"'
rbind-method Class '"bed.matrix"'
read.bed.matrix Read a 'bed.matrix'
read.vcf Create a 'bed.matrix' from VCF files
reshape.GRM Reshape a Genetic Relationship Matrix
score.fixed.linear Score Test for Covariates with Fixed Effects in Linear or Logistic Mixed Model
score.fixed.logistic Score Test for Covariates with Fixed Effects in Linear or Logistic Mixed Model
score.variance.linear Variance Component Test in Linear or Logistic Mixed Model
score.variance.logistic Variance Component Test in Linear or Logistic Mixed Model
select.inds Subsetting from a 'bed.matrix'
select.snps Subsetting from a 'bed.matrix'
set.dist Set Genetic Distance
set.genomic.sex Genomic Sex
set.hwe Hardy-Weinberg Equilibrium
set.stats Basic statistics for a 'bed.matrix'
set.stats.ped Basic statistics for a 'bed.matrix'
set.stats.snps Basic statistics for a 'bed.matrix'
show-method Class '"bed.matrix"'
sigma Class '"bed.matrix"'
sigma-method Class '"bed.matrix"'
sigma<- Class '"bed.matrix"'
sigma<--method Class '"bed.matrix"'
SNP.duplicated Duplicated SNPs
SNP.match SNP matching
SNP.rm.duplicates Remove duplicated SNPs
standardize Class '"bed.matrix"'
standardize-method Class '"bed.matrix"'
standardize<- Class '"bed.matrix"'
standardize<--method Class '"bed.matrix"'
test.inds Evaluation of a condition on SNPS or individuals in a 'bed.matrix'
test.snps Evaluation of a condition on SNPS or individuals in a 'bed.matrix'
TTN TTN data set
TTN.bim TTN data set
TTN.fam TTN data set
TTN.gen TTN data set
TTN.pop TTN data set
which.inds Evaluation of a condition on SNPS or individuals in a 'bed.matrix'
which.snps Evaluation of a condition on SNPS or individuals in a 'bed.matrix'
write.bed.matrix Save a 'bed.matrix'
[-method Class '"bed.matrix"'