Statistical Tools for Quantitative Genetic Analyses

Documentation for package ‘qgg’ version 1.1.6

acc	Compute prediction accuracy for a quantitative or binary trait
adjStat	Adjustment of marker summary statistics using clumping and thresholding
gbayes	Bayesian linear regression models
getG	Get elements from genotype matrix stored in PLINK bedfiles
gfilter	Filter genetic marker data based on different quality measures
glma	Single marker association analysis using linear models or linear mixed models
gmap	Finemapping using Bayesian Linear Regression Models
gprep	Prepare genotype data for all statistical analyses
greml	Genomic rescticted maximum likelihood (GREML) analysis
grm	Computing the genomic relationship matrix (GRM)
gscore	Genomic scoring based on single marker summary statistics
gsea	Gene set enrichment analysis
gsim	Genomic simulation
gsolve	Solve linear mixed model equations
ldsc	LD score regression
magma	Bayesian Multi-marker Analysis of Genomic Annotation (Bayesian MAGMA)
mtadj	Adjustment of marker effects using correlated trait information
pops	Bayesian Polygenic Prioritisation Scoring (Bayesian POPS)
vegas	Perform VEGAS Gene-Based Association Analysis