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gaston

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

Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.

Functions (41)

AGT

AGT data set

Dominance Matrix

GRM

Genetic Relationship Matrix

LCT

LCT data set

Linkage Disequilibrium

LD.plot

Plot Linkage Disequilibrium

LD.thin

LD thinning

SNP.duplicated

Duplicated SNPs

SNP.match

SNP matching

SNP.rm.duplicates

Remove duplicated SNPs

TTN

TTN data set

Tests

Evaluation of a condition on SNPS or individuals in a bed.matrix

as.bed.matrix

Creation of a bed.matrix

association.test

Association Test

bed.loadings

SNP loadings

bed.matrix-class

Class "bed.matrix"

dupli

Small data set to illustrate SNP.rm.duplicates

gaston-package

gaston

is.autosome

Autosomes and X, Y, MT chromosomes

lik.contour

Contour plot for two parameters likelihood

lmm.aireml

Linear mixed model fitting with AIREML

lmm.diago

Linear mixed model fitting with the diagonalization trick

lmm.diago.likelihood

Likelihood of a linear mixed model

lmm.restricted.likelihood

Likelihood of a linear mixed model

lmm.simu

Linear mixed model data simulation

logistic.mm.aireml

Logistic mixed model fitting with Penalized Quasi-Likelihood / AIREML

manhattan

Manhattan plot

qqplot.pvalues

QQ plot of p-values

random.pm

Random square definite positive matrix

read.bed.matrix

Read a bed.matrix

read.vcf

Create a bed.matrix from VCF files

reshape.GRM

Reshape a Genetic Relationship Matrix

score.fixed

Score Test for Covariates with Fixed Effects in Linear or Logistic Mixed Model

score.variance

Variance Component Test in Linear or Logistic Mixed Model

select.inds

Subsetting from a bed.matrix

select.snps

Subsetting from a bed.matrix

set.dist

Set Genetic Distance

set.genomic.sex

Genomic Sex

set.hwe

Hardy-Weinberg Equilibrium

set.stats

Basic statistics for a bed.matrix

write.bed.matrix

Save a bed.matrix

gaston

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

v1.5.7

GPL-3

Authors

Hervé Perdry [cre, aut, cph], Claire Dandine-Roulland [aut, cph], Deepak Bandyopadhyay [cph] (C++ gzstream class), Lutz Kettner [cph] (C++ gzstream class)

Initial release

2020-09-18

gaston

Functions (41)

gaston

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