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"' |