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

Global functions
%*%,bed.matrix,matrix-method	Man page
%*%,bed.matrix,vector-method	Man page
%*%,matrix,bed.matrix-method	Man page
%*%,vector,bed.matrix-method	Man page
.onAttach	Source code
.onLoad	Source code
AGT	Man page
AGT.bim	Man page
AGT.fam	Man page
AGT.gen	Man page
AGT.pop	Man page
DM	Man page Source code
GRM	Man page Source code
LCT	Man page
LCT.bim	Man page
LCT.fam	Man page
LCT.gen	Man page
LCT.pop	Man page
LD	Man page Source code
LD.clump	Man page Source code
LD.plot	Man page Source code
LD.thin	Man page Source code
SNP.duplicated	Man page Source code
SNP.match	Man page Source code
SNP.rm.duplicates	Man page Source code
TTN	Man page
TTN.bim	Man page
TTN.fam	Man page
TTN.gen	Man page
TTN.pop	Man page
[,bed.matrix,logical,logical,missing-method	Man page
[,bed.matrix,logical,missing,missing-method	Man page
[,bed.matrix,logical,numeric,missing-method	Man page
[,bed.matrix,missing,logical,missing-method	Man page
[,bed.matrix,missing,numeric,missing-method	Man page
[,bed.matrix,numeric,logical,missing-method	Man page
[,bed.matrix,numeric,missing,missing-method	Man page
[,bed.matrix,numeric,numeric,missing-method	Man page
all.eq	Source code
alleles.recoding	Source code
as.bed.matrix	Man page Source code
as.matrix,bed.matrix-method	Man page
association.test	Man page Source code
bed.loadings	Man page Source code
bed.matrix	Man page
bed.matrix-class	Man page
bed.merge.inds	Source code
bed_cbind	Source code
bed_rbind	Source code
cbind	Man page
cbind,bed.matrix-method	Man page
coerce,bed.matrix,matrix-method	Man page
coerce,bed.matrix,vector-method	Man page
coerce,matrix,bed.matrix-method	Man page
coerce,vector,bed.matrix-method	Man page
davies	Source code
dim,bed.matrix-method	Man page
dupli	Man page
dupli.bim	Man page
dupli.gen	Man page
dupli.ped	Man page
dupli.pop	Man page
gaston	Man page
gaston-package	Man page
grm.values	Source code
head,bed.matrix-method	Man page
invert_snp_coding	Source code
is.autosome	Man page Source code
is.chr.mt	Man page Source code
is.chr.x	Man page Source code
is.chr.y	Man page Source code
is.null.df	Source code
lik.contour	Man page Source code
lmm.aireml	Man page Source code
lmm.diago	Man page Source code
lmm.diago.likelihood	Man page Source code
lmm.diago.profile.likelihood	Man page Source code
lmm.profile.restricted.likelihood	Man page Source code
lmm.restricted.likelihood	Man page Source code
lmm.simu	Man page Source code
logistic.mm.aireml	Man page Source code
logp.thinning	Source code
manhattan	Man page Source code
manhattan.thinning	Source code
matrix,data.frameOrNULL,data.frameOrNULL-method	Man page
mu	Man page
mu,bed.matrix-method	Man page
mu<-	Man page
mu<-,bed.matrix-method	Man page
p	Man page
p,bed.matrix-method	Man page
p<-	Man page
p<-,bed.matrix-method	Man page
qqplot.pvalues	Man page Source code
r_check_limit_cores	Source code
random.ortho	Source code
random.pm	Man page Source code
rbind	Man page
rbind,bed.matrix-method	Man page
read.bed.matrix	Man page Source code
read.vcf	Man page Source code
read.vcf.filtered	Source code
reshape.GRM	Man page Source code
score.fixed.linear	Man page Source code
score.fixed.logistic	Man page Source code
score.variance.linear	Man page Source code
score.variance.logistic	Man page Source code
select.inds	Man page Source code
select.snps	Man page Source code
set.dist	Man page Source code
set.genomic.sex	Man page Source code
set.hwe	Man page Source code
set.stats	Man page Source code
set.stats.ped	Man page Source code
set.stats.snps	Man page Source code
set_snp_to_na	Source code
show,bed.matrix-method	Man page
sigma	Man page
sigma,bed.matrix-method	Man page
sigma<-	Man page
sigma<-,bed.matrix-method	Man page
snp.sq	Source code
snp_hz_to_na	Source code
standardize	Man page
standardize,bed.matrix-method	Man page
standardize<-	Man page
standardize<-,bed.matrix-method	Man page
test.inds	Man page Source code
test.snps	Man page Source code
trans.X	Source code
void_ped_stats	Source code
void_snps_stats	Source code
which.inds	Man page Source code
which.snps	Man page Source code
write.bed.matrix	Man page Source code