R: GWAS for Multiple Observations on Related Individuals

# GWAS for Multiple Observations on Related Individuals

## Documentation for package ‘RepeatABEL’ version 2.0

- DESCRIPTION file
- Package NEWS

## Help Pages

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