gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Version 1.4.9

Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).

AuthorHervé Perdry & Claire Dandine-Roulland
Date of publication2016-11-29 15:08:34
MaintainerHervé Perdry <herve.perdry@u-psud.fr>
LicenseGPL-3
Version1.4.9
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("gaston")

Getting started

Package overview

Popular man pages

GRM: Genetic Relationship Matrix
is.autosome: Autosomes and X, Y, MT chromosomes
LD.plot: Plot Linkage Disequilibrium
lik.contour: Contour plot for two parameters likelihood
lmm.aireml: Linear mixed model fitting with AIREML
logistic.mm.aireml: Logistic mixed model fitting with Penalized Quasi-Likelihood...
TTN: TTN data set
See all...

All man pages Function index File listing

Man pages

AGT: AGT data set
as.bed.matrix: Creation of a bed.matrix
association.test: Association Test
bed.loadings: SNP loadings
bed.matrix-class: Class '"bed.matrix"'
gaston-package: gaston
GRM: Genetic Relationship Matrix
is.autosome: Autosomes and X, Y, MT chromosomes
LCT: LCT data set
LD: Linkage Disequilibrium
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.simu: Linear mixed model data simulation
logistic.mm.aireml: Logistic mixed model fitting with Penalized Quasi-Likelihood...
random.pm: Random square definite positive 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: Score Test for Covariates with Fixed Effects in Linear or...
score.variance: Variance Component Test in Linear or Logistic Mixed Model
select.inds: Subsetting from a 'bed.matrix'
select.snps: Subsetting from a 'bed.matrix'
set.genomic.sex: Genomic Sex
set.hwe: Hardy-Weinberg Equilibrium
set.stats: Basic statistics for a 'bed.matrix'
TTN: TTN data set
write.bed.matrix: Save a 'bed.matrix'

Functions

AGT Man page
AGT.bim Man page
AGT.fam Man page
AGT.gen Man page
AGT.pop Man page
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.plot Man page Source code
LD.thin 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
\%*\%,bed.matrix,matrix-method Man page
\%*\%,bed.matrix,vector-method Man page
\%*\%,matrix,bed.matrix-method Man page
\%*\%,vector,bed.matrix-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
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
count.vcf Source code
davies Source code
dim,bed.matrix-method Man page
gaston Man page
gaston-package Man page
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.simu Man page Source code
logistic.mm.aireml Man page 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
onLoad Source code
p Man page
p,bed.matrix-method Man page
p<- Man page
p<-,bed.matrix-method Man page
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
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.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
void_ped_stats Source code
void_snps_stats Source code
write.bed.matrix Man page Source code

Files

TODO
inst
inst/extdata
inst/extdata/LCT.bim
inst/extdata/chr2.rds
inst/extdata/LCT.vcf.gz
inst/extdata/LCT.bed
inst/extdata/chr2.bed
inst/extdata/LCT.vcf.gz.tbi
inst/extdata/LCT.fam
inst/extdata/LCT.rds
inst/doc
inst/doc/gaston.Rnw
inst/doc/gaston.pdf
inst/doc/gaston.R
src
src/export-aireml-1k.cpp
src/m4_transpose.cpp
src/any.h
src/Makevars
src/ai-reml-nk.h
src/m4_recode.cpp
src/ai-reml-logit-nk-covar.h
src/diago.h
src/ai-reml-logit-nk.h
src/export-aireml-nk.cpp
src/m4_extractind.cpp
src/ai-reml-logit-1k.h
src/optimize.cpp
src/m4_kinship_type.h
src/m4_extractsnp.cpp
src/loubar.h
src/matrix-varia.h
src/m4_prod_p.cpp
src/m4_ld.h
src/m4_ldthin_right.cpp
src/gwas_lmm_diago_lrt_mt.cpp
src/diago_wrapers.h
src/gwas_lmm_diago_wald.cpp
src/lmm_diago_nocovar.cpp
src/m4_prod2_ms.cpp
src/m4_bed.cpp
src/m4_exports.cpp
src/m4_ldp.cpp
src/m4_bind_inds.cpp
src/optimize.h
src/m4_ldthin_left.cpp
src/m4_bind_snps.cpp
src/diago_full.h
src/ai-reml-1k-covar.h
src/export-aireml-logit-1k.cpp
src/diago_nocovar.h
src/davies.c
src/ai-reml-logit-1k-covar.h
src/lmm_diago_full.cpp
src/m4_stats.cpp
src/isnullptr.cpp
src/gwas_lmm_diago_lrt.cpp
src/m4_read_vcf.cpp
src/matrix4.cpp
src/export-aireml-logit-nk.cpp
src/m4_prod2_p.cpp
src/ai-reml-1k.h
src/matrix-varia.cpp
src/m4_conversion.cpp
src/loubar.cpp
src/m4_prod_ms.cpp
src/ai-reml-nk-covar.h
src/m4_dims.cpp
src/diago_full_nocovar.h
src/m4_ld.cpp
src/hwe_chi.cpp
src/Makevars.win
src/gwas_lm_quanti.cpp
src/lmm_diago.cpp
src/hwe.cpp
src/m4_kinship_p.cpp
src/m4_ldthin_random.cpp
src/matrix4.h
src/diago_wrapers.cpp
src/gwas_lmm_score.cpp
src/gwas_lmm_diago_wald_mt.cpp
src/m4_kinship.cpp
NAMESPACE
NEWS
data
data/AGT.rda
data/datalist
data/TTN.rda
data/LCT.rda
R
R/bm_stats.r
R/bm_files.r
R/bm_as_bm.r
R/bm_genomic_sex.r
R/bm_subsetting.r
R/score.r
R/bm_ld.r
R/random_pm.r
R/bm_product.r
R/bm_grm.r
R/lmm_diago.r
R/lmm_aireml.r
R/bm_hwe.r
R/bm_ld_thinner.r
R/bm_bind.r
R/gwas.r
R/bm_select.r
R/ld_plot_exemple.r
R/zzz.r
R/bm_interface.r
R/logistic_mm_aireml.r
R/lmm_simu.r
R/ld_plot.r
R/lik_contour.r
R/bm_merge.r
R/bm.r
vignettes
vignettes/gaston-033.pdf
vignettes/gaston-028.pdf
vignettes/gaston-041.pdf
vignettes/gaston-016.pdf
vignettes/gaston.Rnw
vignettes/gaston-053.pdf
vignettes/gaston-044.pdf
vignettes/gaston-030.pdf
vignettes/gaston-015.pdf
vignettes/gaston-048.pdf
vignettes/gaston-052.pdf
vignettes/gaston-039.pdf
vignettes/gaston-042.pdf
vignettes/gaston-037.pdf
vignettes/gaston-040.pdf
vignettes/gaston-056.pdf
vignettes/gaston-029.pdf
vignettes/gaston-054.pdf
vignettes/gaston-026.pdf
vignettes/gaston-055.pdf
MD5
build
build/vignette.rds
DESCRIPTION
man
man/LD.Rd
man/read.bed.matrix.Rd
man/TTN.Rd
man/GRM.Rd
man/AGT.Rd
man/lmm.diago.Rd
man/score.variance.Rd
man/random.pm.Rd
man/set.hwe.Rd
man/association.test.Rd
man/is.autosome.Rd
man/bed.matrix-class.Rd
man/read.vcf.Rd
man/set.genomic.sex.Rd
man/select.inds.Rd
man/bed.loadings.Rd
man/reshape.GRM.Rd
man/gaston-package.Rd
man/lik.contour.Rd
man/logistic.mm.aireml.Rd
man/set.stats.Rd
man/lmm.diago.likelihood.Rd
man/LD.plot.Rd
man/LD.thin.Rd
man/as.bed.matrix.Rd
man/write.bed.matrix.Rd
man/lmm.simu.Rd
man/score.fixed.Rd
man/lmm.aireml.Rd
man/LCT.Rd
man/select.snps.Rd
gaston documentation built on May 19, 2017, 10:04 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

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