Create_gwaa_data2       Creates a gwaa.data2 object
Create_gwaa_scan2       Creates a scan.gwaa2 object
SmoothSNPmatrix         Imputes column means to missing genotypes
chromosome              Extracts the chromosome numbers
compute.GRM             Computes a Genetic Relationship Matrix from a
                        GenABEL-like object
constructV              Constructs the (co)variance matrix for y
estlambda               Function to estimate lambda
gwaa.data2-class        An S4 class to represent GWAS input data
idnames                 Extracts the id names
keep_gwaa_data          A function to subset an gwaa.data2 object
map                     Extracts the map information
nids                    Extracts the number of ids
plot.scan.gwaa2         Function to plot P-values as a Manhattan plot
preFitModel             Fits a linear mixed model (without fixed SNP
                        effects) and computes the fitted
                        variance-covariance matrix for later use in the
                        rGLS function.
rGLS                    GWAS for Studies having Repeated Measurements
                        on Related Individuals
scan.gwaa2-class        An S4 class to represent SNP data
simulate_PhenData       Simulation function for the RepeatABEL package.
simulate_gendata        Function to simulate genotype data for the
                        RepeatABEL package.
snp.data                An S4 class to represent SNP data
snpnames                Extracts the snpnames
summary.scan.gwaa2      Summary function for the rGLS output
