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gaston (version 1.1)

Genetic Data Manipulation (Quality Control, GRM and LD Computations, PCA), Linear Mixed Models (AIREML Algorithm), Association Testing

Description

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

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Version

Install

install.packages('gaston')

Monthly Downloads

9,627

Version

1.1

License

GPL-3

Maintainer

Herve Perdry

Last Published

October 2nd, 2015

Functions in gaston (1.1)

LD

Linkage Disequilibrium
bed.loadings

SNP loadings
select.inds

Subsetting from a bed.matrix
TTN

TTN data set
GRM

Genetic Relationship Matrix
write.bed.matrix

Save a bed.matrix
association.test

Association Test
select.snps

Subsetting from a bed.matrix
read.bed.matrix

Read a bed.matrix
random.pm

Random square definite positive matrix
lmm.simu

Linear mixed model data simulation
gaston-package

gaston
set.stats

Basic statistics for a bed.matrix
set.hwe

Hardy-Weinberg Equilibrium
bed.matrix-class

Class "bed.matrix"
read.vcf

Create a bed.matrix from VCF files
AGT

AGT data set
lik.contour

Contour plot for two parameters likelihood
lmm.aireml

Linear mixed model fitting with AIREML
LD.thin

LD thinning
LCT

LCT data set
lmm.diago.likelihood

Likelihood of a linear mixed model
lmm.diago

Linear mixed model fitting with the diagonalization trick