# Complementary Genomic Functions

## Documentation for package ‘ASRgenomics’ version 1.1.6

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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