Package: ASRgenomics 1.1.4

ASRgenomics: Complementary Genomic Functions

Presents a series of molecular and genetic routines in the R environment with the aim of assisting in analytical pipelines before and after the use of 'asreml' or another library to perform analyses such as Genomic Selection or Genome-Wide Association Analyses. Methods and examples are described in Gezan, Oliveira, Galli, and Murray (2022) <https://asreml.kb.vsni.co.uk/wp-content/uploads/sites/3/ASRgenomics_Manual.pdf>.

Authors:Salvador Gezan [aut, cre], Darren Murray [aut], Amanda Avelar de Oliveira [aut], Giovanni Galli [aut], VSN International [cph]

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ASRgenomics.pdf |ASRgenomics.html✨
ASRgenomics/json (API)
NEWS

# Install 'ASRgenomics' in R:
install.packages('ASRgenomics', repos = c('https://sgezan.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • geno.apple - Genotypic data for apple dataset
  • geno.pine655 - Genotypic data of 655 genotypes for loblolly pine dataset
  • geno.pine926 - Genotypic data of 926 genotypes for loblolly pine dataset
  • geno.salmon - Genotypic data for Atlantic salmon dataset
  • ped.pine - Pedigree data for loblolly pine dataset
  • ped.salmon - Pedigree data for Atlantic salmon dataset
  • pheno.apple - Phenotypic data for apple dataset
  • pheno.pine - Phenotypic data for loblolly pine dataset
  • pheno.salmon - Phenotypic data for Atlantic salmon dataset

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

18 exports 1 stars 0.23 score 117 dependencies 8 scripts 566 downloads

Last updated 8 months agofrom:c211460e41. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-winOKAug 28 2024
R-4.5-linuxOKAug 28 2024
R-4.4-winOKAug 28 2024
R-4.4-macOKAug 28 2024
R-4.3-winOKAug 28 2024
R-4.3-macOKAug 28 2024

Exports:full2sparseG.inverseG.matrixG.predictG.tuneupH.inverseH.matrixkinship.diagnosticskinship.heatmapkinship.pcamatch.G2Amatch.kinship2phenoqc.filteringsnp.pcasnp.pruningsnp.recodesparse2fullsynthetic.cross

Dependencies:abindAGHmatrixbackportsbase64encbootbroombslibcachemcarcarDatacliclustercolorspacecorrplotcowplotcpp11crayoncrosstalkdata.tabledendextendDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomefsgenericsggdendroggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplyrpolynompromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownrstatixsassscalesscattermorescatterplot3dSparseMstringistringrsuperheatsurvivaltibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Generates a sparse form matrix from a full form matrixfull2sparse
Obtains the inverse of the genomic relationship matrix GG.inverse
Obtains the genomic matrix from SNP data for additive or dominant relationshipsG.matrix
Generates the conditional predictions of random effects (BLUPs)G.predict
Tune-up the the genomic relationship matrix GG.tuneup
Genotypic data for apple datasetgeno.apple
Genotypic data of 655 genotypes for loblolly pine datasetgeno.pine655
Genotypic data of 926 genotypes for loblolly pine datasetgeno.pine926
Genotypic data for Atlantic salmon datasetgeno.salmon
Generates the inverse of the hybrid H matrixH.inverse
Generates the hybrid H matrixH.matrix
Reports summary statistics, plots and filter options for a given kinship matrix Kkinship.diagnostics
Enhanced heatmap plot for a kinship matrix Kkinship.heatmap
Performs a Principal Component Analysis (PCA) based on a kinship matrix Kkinship.pca
Check the genomic relationship matrix G against the pedigree relationship matrix A or vice versamatch.G2A
Check any kinship matrix K against phenotypic datamatch.kinship2pheno
Pedigree data for loblolly pine datasetped.pine
Pedigree data for Atlantic salmon datasetped.salmon
Phenotypic data for apple datasetpheno.apple
Phenotypic data for loblolly pine datasetpheno.pine
Phenotypic data for Atlantic salmon datasetpheno.salmon
Quality control filtering of molecular matrix M for downstream analysesqc.filtering
Performs a Principal Component Analysis (PCA) based on a molecular matrix Msnp.pca
Reduces the number of redundant markers on a molecular matrix M by pruningsnp.pruning
Recodes the molecular matrix M for downstream analysessnp.recode
Generates a full matrix form from a sparse form matrixsparse2full
Generates a molecular matrix M for hypothetical crosses based on the genomic information of the parentssynthetic.cross