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ASRgenomics

This package presents a series of molecular and genetic routines in the R environment with the aim of assisting in analytical pipelines before and after use of ASReml-R or another library to perform analyses such as Genomic Selection (GS) or Genome-Wide Association Analyses (GWAS)

Installation

Use the following code to download and install ASRgenomics:

install.packages("remotes")
remotes::install_github("asrtools/asrgenomics")

Usage

To load the library use:

library(ASRgenomics)

Authors

This package has been developed by the VSN International team (https://vsni.co.uk/)

Developers

Maintenance

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Version

Install

install.packages('ASRgenomics')

Monthly Downloads

806

Version

1.1.4

License

MIT + file LICENSE

Maintainer

Salvador Gezan

Last Published

January 29th, 2024

Functions in ASRgenomics (1.1.4)

geno.pine926

Genotypic data of 926 genotypes for loblolly pine dataset
dummy.map_

Creates a dummy map if not provided
full2sparse

Generates a sparse form matrix from a full form matrix
match.G2A

Check the genomic relationship matrix G against the pedigree relationship matrix A or vice versa
maf

Estimates minor allele frequency (MAF)
check.args_

Check string arguments
kinship.heatmap

Enhanced heatmap plot for a kinship matrix K
kinship.pca

Performs a Principal Component Analysis (PCA) based on a kinship matrix K
check.data.mode_

Check data mode
G.tuneup

Tune-up the the genomic relationship matrix G
check.data_

Check data class
silent_

Function that silences everything (e.g., cat(), print(), message(), ...)
qc.filtering

Quality control filtering of molecular matrix M for downstream analyses
heterozygosity

Estimates observed and expected heterozygosity
geno.salmon

Genotypic data for Atlantic salmon dataset
ped.pine

Pedigree data for loblolly pine dataset
match.kinship2pheno

Check any kinship matrix K against phenotypic data
check.logical_

Check logical arguments
kinship.diagnostics

Reports summary statistics, plots and filter options for a given kinship matrix K
sparse2full

Generates a full matrix form from a sparse form matrix
snp.recode

Recodes the molecular matrix M for downstream analyses
synthetic.cross

Generates a molecular matrix M for hypothetical crosses based on the genomic information of the parents
pheno.pine

Phenotypic data for loblolly pine dataset
pheno.salmon

Phenotypic data for Atlantic salmon dataset
geno.pine655

Genotypic data of 655 genotypes for loblolly pine dataset
snp.pruning

Reduces the number of redundant markers on a molecular matrix M by pruning
snp.pca

Performs a Principal Component Analysis (PCA) based on a molecular matrix M
pheno.apple

Phenotypic data for apple dataset
ped.salmon

Pedigree data for Atlantic salmon dataset
geno.apple

Genotypic data for apple dataset
H.matrix

Generates the hybrid \(H\) matrix
Kinv.condition

Assess condition of the inverse of K
G.matrix

Obtains the genomic matrix from SNP data for additive or dominant relationships
H.inverse

Generates the inverse of the hybrid H matrix
G.predict

Generates the conditional predictions of random effects (BLUPs)
G.inverse

Obtains the inverse of the genomic relationship matrix G
ASRgenomics-package

ASRgenomics: Complementary Genomic Functions
Fis

Estimates the population level inbreeding (Fis) by marker
callrate

Estimates call rate