ASRgenomics1.1.5 package

ASRgenomics: Complementary Genomic Functions

Estimates call rate

Check string arguments

Check data mode

Check data class

Check logical arguments

Creates a dummy map if not provided

Estimates the population level inbreeding (Fis) by marker

Generates a sparse form matrix from a full form matrix

Obtains the inverse of the genomic relationship matrix G

Obtains the genomic matrix from SNP data for additive or dominant rela...

Generates the conditional predictions of random effects (BLUPs)

Tune-up the the genomic relationship matrix G

Generates the inverse of the hybrid H matrix

Generates the hybrid $H$ matrix

Estimates observed and expected heterozygosity

Reports summary statistics, plots and filter options for a given kinsh...

Enhanced heatmap plot for a kinship matrix K

Performs a Principal Component Analysis (PCA) based on a kinship matri...

Assess condition of the inverse of K

Estimates minor allele frequency (MAF)

Check the genomic relationship matrix G against the pedigree relations...

Check any kinship matrix K against phenotypic data

Quality control filtering of molecular matrix M for downstream analyse...

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

Performs a Principal Component Analysis (PCA) based on a molecular mat...

Reduces the number of redundant markers on a molecular matrix M by pru...

Recodes the molecular matrix M for downstream analyses

Generates a full matrix form from a sparse form matrix

Generates a molecular matrix M for hypothetical crosses based on the g...