Statistical Tools for Quantitative Genetic Analyses

Documentation for package ‘qgg’ version 1.0.4

adjLD	LD pruning of summary statistics
gbayes	Genomic prediction models implemented using Bayesian Methods (small data)
gblup	Compute Genomic BLUP values
getGRM	Extract elements from genomic relationship matrix (GRM) stored on disk
getW	Extract elements from genotype matrix (W) stored on disk
gprep	Prepare genotype data for all statistical analyses (initial step)
greml	Genomic REML analysis
grm	Computing the genomic relationship matrix (GRM)
gscore	Genomic prediction based on single marker summary statistics
gsea	Gene set enrichment analysis
gsolve	Genomic prediction based on a linear mixed model
lma	Single marker association analysis using linear models or linear mixed models
mergeGRM	Merge multiple GRMlist objects
qgg	Implements Genomic Feature Linear Mixed Models using Likelihood or Bayesian Methods