| ASRgenomics {ASRgenomics} | R Documentation |
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).
The main tasks considered are:
Preparing and exploring pedigree, phenotypic and genomic data.
Calculating and evaluating genomic matrices and their inverse.
Complementing and expanding results from genomic analyses.
The functions implemented consider aspects such as: filtering SNP data for
quality control; assessing a kinship matrix \boldsymbol{K} by
reporting diagnostics (statistics and plots); performing Principal
Component Analyses (PCA) based on
kinship or SNP matrices for understanding population structure;
calculating the genomic matrix \boldsymbol{G} and its inverse
and assessing their quality; matching pedigree- against genomic-based matrices;
tuning up a genomic matrix (bend, blend or align); and obtaining the hybrid
matrix \boldsymbol{H} as required with single-step GBLUP (ssGBLUP).
For the full manual please visit: https://asreml.kb.vsni.co.uk/wp-content/uploads/sites/3/ASRgenomics_Manual.pdf