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

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

## Documentation for package ‘gaston’ version 1.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"'