GWAS for Multiple Observations on Related Individuals

Documentation for package ‘RepeatABEL’ version 2.0

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
Create_gwaa_data2	Creates a gwaa.data2 object
Create_gwaa_scan2	Creates a scan.gwaa2 object
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_gendata	Function to simulate genotype data for the RepeatABEL package.
simulate_PhenData	Simulation function for the RepeatABEL package.
SmoothSNPmatrix	Imputes column means to missing genotypes
snp.data	An S4 class to represent SNP data
snpnames	Extracts the snpnames
summary.scan.gwaa2	Summary function for the rGLS output