Learn R Programming
⚠️There's a newer version (1.4.9) of this package.Take me there.

gaston (version 1.0)

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).

Copy Link

Version

Install

install.packages('gaston')

Monthly Downloads

5,792

Version

1.0

License

GPL-3

Maintainer

Herve Perdry

Last Published

October 1st, 2015

Functions in gaston (1.0)

set.hwe

Hardy-Weinberg Equilibrium
LD

Linkage Disequilibrium
bed.matrix-class

Class "bed.matrix"
set.stats

Basic statistics for a bed.matrix
select.snps

Subsetting from a bed.matrix
GRM

Genetic Relationship Matrix
association.test

Association Test
lik.contour

Contour plot for two parameters likelihood
read.bed.matrix

Read a bed.matrix
LCT

LCT data set
write.bed.matrix

Save a bed.matrix
random.pm

Random square definite positive matrix
TTN

TTN data set
lmm.diago

Linear mixed model fitting with the diagonalization trick
LD.thin

LD thinning
AGT

AGT data set
select.inds

Subsetting from a bed.matrix
lmm.simu

Linear mixed model data simulation
lmm.aireml

Linear mixed model fitting with AIREML
lmm.diago.likelihood

Likelihood of a linear mixed model
gaston-package

gaston
read.vcf

Create a bed.matrix from VCF files
bed.loadings

SNP loadings