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).

Author
Hervé Perdry & Claire Dandine-Roulland
Date of publication
2016-11-29 15:08:34
Maintainer
Hervé Perdry <herve.perdry@u-psud.fr>
License
GPL-3
Version
1.4.9

View on CRAN

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'

Files in this package

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