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gaston (version 1.3.1)

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

5,792

Version

1.3.1

License

GPL-3

Maintainer

Herve Perdry

Last Published

December 15th, 2015

Functions in gaston (1.3.1)

read.bed.matrix

Read a bed.matrix
LD.thin

LD thinning
AGT

AGT data set
lik.contour

Contour plot for two parameters likelihood
bed.matrix-class

Class "bed.matrix"
select.inds

Subsetting from a bed.matrix
GRM

Genetic Relationship Matrix
random.pm

Random square definite positive matrix
set.hwe

Hardy-Weinberg Equilibrium
bed.loadings

SNP loadings
lmm.diago.likelihood

Likelihood of a linear mixed model
LCT

LCT data set
lmm.simu

Linear mixed model data simulation
lmm.diago

Linear mixed model fitting with the diagonalization trick
read.vcf

Create a bed.matrix from VCF files
select.snps

Subsetting from a bed.matrix
LD

Linkage Disequilibrium
TTN

TTN data set
association.test

Association Test
write.bed.matrix

Save a bed.matrix
gaston-package

gaston
lmm.aireml

Linear mixed model fitting with AIREML
set.stats

Basic statistics for a bed.matrix