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).

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

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

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

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