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

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

Install the latest version of this package by entering the following in R:
install.packages("gaston")
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

View on CRAN

Functions

AGT Man page
AGT.bim Man page
AGT.fam Man page
AGT.gen Man page
AGT.pop Man page
as.bed.matrix Man page
as.matrix,bed.matrix-method Man page
association.test Man page
bed.loadings Man page
bed.matrix Man page
bed.matrix-class 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,matrix-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,vector-method Man page
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
dim,bed.matrix-method Man page
gaston Man page
gaston-package Man page
GRM Man page
head,bed.matrix-method Man page
is.autosome Man page
is.chr.mt Man page
is.chr.x Man page
is.chr.y Man page
LCT Man page
LCT.bim Man page
LCT.fam Man page
LCT.gen Man page
LCT.pop Man page
LD Man page
LD.plot Man page
LD.thin Man page
lik.contour Man page
lmm.aireml Man page
lmm.diago Man page
lmm.diago.likelihood Man page
lmm.simu Man page
logistic.mm.aireml Man page
\%*\%,matrix,bed.matrix-method Man page
matrix,data.frameOrNULL,data.frameOrNULL-method Man page
mu Man page
mu<- Man page
mu<-,bed.matrix-method Man page
mu,bed.matrix-method Man page
p Man page
p<- Man page
p<-,bed.matrix-method Man page
p,bed.matrix-method Man page
random.pm Man page
rbind Man page
rbind,bed.matrix-method Man page
read.bed.matrix Man page
read.vcf Man page
reshape.GRM Man page
score.fixed.linear Man page
score.fixed.logistic Man page
score.variance.linear Man page
score.variance.logistic Man page
select.inds Man page
select.snps Man page
set.genomic.sex Man page
set.hwe Man page
set.stats Man page
set.stats.ped Man page
set.stats.snps Man page
show,bed.matrix-method Man page
sigma Man page
sigma<- Man page
sigma<-,bed.matrix-method Man page
sigma,bed.matrix-method Man page
standardize Man page
standardize<- Man page
standardize<-,bed.matrix-method Man page
standardize,bed.matrix-method Man page
TTN Man page
TTN.bim Man page
TTN.fam Man page
TTN.gen Man page
TTN.pop Man page
\%*\%,vector,bed.matrix-method Man page
write.bed.matrix Man page

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

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

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

All documentation is copyright its authors; we didn't write any of that.