Froh_inbreeding         Function to calculated Froh genome-wide or
                        chromosome-wide
Froh_inbreedingClass    Function to calculated Froh using a ROH-class
consecutiveRUNS.run     Main function to detect genomic RUNS
                        (ROHom/ROHet) using the consecutive method
consecutiveRunsCpp      Function to detect consecutive runs in a vector
                        (individual's genotypes)
createRUNdf             Function to create a dataframe of RUNS per
                        individual animal Requires a map file (other
                        filename to read or R object) Parameters on
                        maximum number of missing and opposite
                        genotypes in the run (not the window) are
                        implemented here
findOppositeAndMissing
                        Function to calculate
                        oppositeAndMissingGenotypes array
genoConvertCpp          Convert 0/1/2 genotypes to 0/1
heteroZygotTest         Function to check whether a window is (loosely)
                        heterozygous or not
heteroZygotTestCpp      Function to check whether a window is (loosely)
                        heterozygous or not
homoZygotTest           Function to check whether a window is (loosely)
                        homozygous or not
homoZygotTestCpp        Function to check whether a window is (loosely)
                        homozygous or not
pedConvertCpp           Convert ped genotypes to 0/1
plot_DistributionRuns   Plot Distribution of runs
plot_InbreedingChr      Plot Froh-based inbreeding coefficients by
                        group
plot_PatternRuns        Plot sum of run-lengths (or average
                        run-lengths) against the number of runs per
                        individual
plot_Runs               Function to plot runs per individual
plot_SnpsInRuns         Plot the number of times each SNP falls inside
                        runs
plot_StackedRuns        Plot stacked runs
plot_ViolinRuns         Violin plot of run length per individual
                        (either sum or mean)
plot_manhattanRuns      Plot the proportion of times SNPs are inside
                        runs - MANHATTAN PLOT
readExternalRuns        Read runs from external files
readPOPCpp              Function to return a dataframe of population
                        (POP, ID)
reorderDF               Function to reorder data frames by CHROMOSOME
slidingRUNS.run         Main function to detect RUNS (ROHom/ROHet)
                        using sliding windows (a la Plink)
slidingWindow           Function to slide a window over a vector
                        (individual's genotypes)
slidingWindowCpp        Function to slide a window over a vector
                        (individual's genotypes)
snpInRun                Function to return a vector of T/F for whether
                        a SNP is or not in a RUN
snpInRunCpp             Function to return a vector of T/F for whether
                        a SNP is or not in a RUN
snpInsideRuns           Function to count number of times a SNP is in a
                        RUN
snpInsideRunsCpp        Function to count number of times a SNP is in a
                        RUN
summaryRuns             Summary statistics on detected runs
tableRuns               Function to retrieve most common runs in the
                        population
writeRUN                Function to write out RUNS per individual
                        animal
