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

gaston (version 1.4.8)

Genetic Data Manipulation (Quality Control, GRM and LD Computations, PCA), Linear and Logistic 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, diagonalization trick).

Copy Link

Version

Install

install.packages('gaston')

Monthly Downloads

9,627

Version

1.4.8

License

GPL-3

Maintainer

Herve Perdry

Last Published

November 5th, 2016

Functions in gaston (1.4.8)

AGT

AGT data set
LD

Linkage Disequilibrium
bed.matrix-class

Class "bed.matrix"
association.test

Association Test
GRM

Genetic Relationship Matrix
LCT

LCT data set
bed.loadings

SNP loadings
gaston-package

gaston
as.bed.matrix

Creation of a bed.matrix
is.autosome

Autosomes and X, Y, MT chromosomes
lmm.simu

Linear mixed model data simulation
read.vcf

Create a bed.matrix from VCF files
read.bed.matrix

Read a bed.matrix
lik.contour

Contour plot for two parameters likelihood
lmm.diago.likelihood

Likelihood of a linear mixed model
lmm.diago

Linear mixed model fitting with the diagonalization trick
LD.plot

Plot Linkage Disequilibrium
LD.thin

LD thinning
random.pm

Random square definite positive matrix
lmm.aireml

Linear mixed model fitting with AIREML
write.bed.matrix

Save a bed.matrix
set.hwe

Hardy-Weinberg Equilibrium
score.variance.linear/score.variance.logistic

Variance Component Test in Linear or Logistic Mixed Model
reshape.GRM

Reshape a Genetic Relationship Matrix
select.snps

Subsetting from a bed.matrix
TTN

TTN data set
select.inds

Subsetting from a bed.matrix
set.stats

Basic statistics for a bed.matrix
score.fixed.linear/score.fixed.logistic

Score Test for Covariates with Fixed Effects in Linear or Logistic Mixed Model
set.genomic.sex

Genomic Sex