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gaston (version 1.4.9)

Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Description

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

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Version

Install

install.packages('gaston')

Monthly Downloads

4,260

Version

1.4.9

License

GPL-3

Maintainer

Herve Perdry

Last Published

November 29th, 2016

Functions in gaston (1.4.9)

LD

Linkage Disequilibrium
LCT

LCT data set
bed.loadings

SNP loadings
LD.thin

LD thinning
association.test

Association Test
LD.plot

Plot Linkage Disequilibrium
read.vcf

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

Read a bed.matrix
set.stats

Basic statistics for a bed.matrix
lmm.aireml

Linear mixed model fitting with AIREML
as.bed.matrix

Creation of a bed.matrix
lik.contour

Contour plot for two parameters likelihood
AGT

AGT data set
set.hwe

Hardy-Weinberg Equilibrium
TTN

TTN data set
write.bed.matrix

Save a bed.matrix
set.genomic.sex

Genomic Sex
select.snps

Subsetting from a bed.matrix
score.fixed.linear/score.fixed.logistic

Score Test for Covariates with Fixed Effects in Linear or Logistic Mixed Model
bed.matrix-class

Class "bed.matrix"
lmm.diago.likelihood

Likelihood of a linear mixed model
lmm.diago

Linear mixed model fitting with the diagonalization trick
gaston-package

gaston
reshape.GRM

Reshape a Genetic Relationship Matrix
random.pm

Random square definite positive matrix
lmm.simu

Linear mixed model data simulation
select.inds

Subsetting from a bed.matrix
is.autosome

Autosomes and X, Y, MT chromosomes
GRM

Genetic Relationship Matrix
score.variance.linear/score.variance.logistic

Variance Component Test in Linear or Logistic Mixed Model