Complementary Genomic Functions

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Documentation for package ‘ASRgenomics’ version 1.1.4

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full2sparse Generates a sparse form matrix from a full form matrix
G.inverse Obtains the inverse of the genomic relationship matrix G
G.matrix Obtains the genomic matrix from SNP data for additive or dominant relationships
G.predict Generates the conditional predictions of random effects (BLUPs)
G.tuneup Tune-up the the genomic relationship matrix G
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
H.inverse Generates the inverse of the hybrid H matrix
H.matrix Generates the hybrid H matrix
kinship.diagnostics Reports summary statistics, plots and filter options for a given kinship matrix K
kinship.heatmap Enhanced heatmap plot for a kinship matrix K
kinship.pca Performs a Principal Component Analysis (PCA) based on a kinship matrix K
match.G2A Check the genomic relationship matrix G against the pedigree relationship matrix A or vice versa
match.kinship2pheno Check any kinship matrix K against phenotypic data
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
qc.filtering Quality control filtering of molecular matrix M for downstream analyses
snp.pca Performs a Principal Component Analysis (PCA) based on a molecular matrix M
snp.pruning Reduces the number of redundant markers on a molecular matrix M by pruning
snp.recode Recodes the molecular matrix M for downstream analyses
sparse2full Generates a full matrix form from a sparse form matrix
synthetic.cross Generates a molecular matrix M for hypothetical crosses based on the genomic information of the parents