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gaston (version 1.2)

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

5,792

Version

1.2

License

GPL-3

Maintainer

Herve Perdry

Last Published

November 10th, 2015

Functions in gaston (1.2)

LD.thin

LD thinning
lmm.simu

Linear mixed model data simulation
write.bed.matrix

Save a bed.matrix
AGT

AGT data set
GRM

Genetic Relationship Matrix
TTN

TTN data set
lmm.diago

Linear mixed model fitting with the diagonalization trick
read.bed.matrix

Read a bed.matrix
LD

Linkage Disequilibrium
lik.contour

Contour plot for two parameters likelihood
select.snps

Subsetting from a bed.matrix
random.pm

Random square definite positive matrix
set.hwe

Hardy-Weinberg Equilibrium
association.test

Association Test
bed.matrix-class

Class "bed.matrix"
lmm.aireml

Linear mixed model fitting with AIREML
set.stats

Basic statistics for a bed.matrix
bed.loadings

SNP loadings
gaston-package

gaston
LCT

LCT data set
select.inds

Subsetting from a bed.matrix
lmm.diago.likelihood

Likelihood of a linear mixed model
read.vcf

Create a bed.matrix from VCF files