cbindFiles              Combine a sequence of files by columns
finishParallelRun       Closing the Rmpi cluster
genDataGetPart          Extracting part of genetic data.
genDataLoad             Loading the data previously read in and saved
                        by "genDataRead"
genDataPreprocess       Pre-processing of the genetic data
genDataRead             Reading the genetic data from a file
getChildren             Getter for all rows with children data
getDyads                Getter only for all dyads (child and one
                        parent)
getFathers              Getter for all rows with fathers' data
getFullTriads           Getter for all full triads
getMothers              Getter for all rows with mothers' data
gxe                     Test for gene-environment interaction
hapPower                Power simulation for association analyses with
                        Haplin
hapPowerAsymp           Asymptotic power calculations for genetic
                        association analyses with Haplin
hapRelEff               Relative efficiency comparing different study
                        designs in genetic association analysis with
                        Haplin
hapRun                  Simulates genetic data and runs Haplin for each
                        simulation
hapSim                  Simulation of genetic data in Haplin format
haplin                  Fitting log-linear models to case-parent triad
                        and/or case-control data
haplinSlide             Run haplin analysis in a series of sliding
                        windows over a sequence of markers/SNPs
haplinStrat             Fit 'haplin' to each subset/stratum of data,
                        determined by the argument 'strata'
haptable                Create haplin table
initParallelRun         Initialization of the Rmpi cluster
lineByLine              Line-by-line modification of files
nfam                    Count the number of families in the data
nindiv                  Count the number of individuals in the data
nsnps                   Count the number of markers in the data
output                  Save files with summary, table, and plot from a
                        haplin object.
pQQ                     QQ-plot with confidence intervals for a vector
                        of p-values
plot.haplin             Plot a haplin object
plot.haplinSlide        Plotter function for haplinSlide.
plot.haplinStrat        Plotter function for haplinStrat results.
plot.haptable           Plot a haptable object
plotPValues             Plotting p-values for relative risks
print.haplin            Print a haplin object
print.summary.haplin    Print the summary of a haplin object
rbindFiles              Combine a sequence of files by rows
showGen                 Display chosen genotypes
showPheno               Display phenotype part of data
showSNPnames            Display marker names
snpPos                  Find the column numbers of SNP identifiers/SNP
                        numbers in a ped file
snpPower                Power calculations for a single SNP
snpSampleSize           Sample size calculations for a single SNP
suest                   Compute a joint p-value for a list of haplin
                        fits (usually from a sliding window approach),
                        correcting for multiple testing.
summary.haplin          Summary of a haplin object
toDataFrame             Stack dataframes from haplinSlide into a single
                        dataframe
