XHMM_plots              Make a series of plots documenting the output
                        of XHMM.
calcSegmentIntervals    Determine all of the indices where a transition
                        in value occurs.
listOfNulls             Create an empty list object of given size.
loadNamedVectorNoHeaderMayNotExist
                        Load a vector with named rows.
loadTargetsToGenes      Load the exome-target to gene mappings.
loadXCNVcalls           Load the XHMM CNV calls.
loadXHMMdata            Load all data files generated during an XHMM
                        run.
pedigreeDataToBinarySampleProperties
                        Convert a parsed Plink/Seq pedinfo file into a
                        matrix of binary sample properties.
phenotypeDataToBinarySampleProperties
                        Convert a parsed Plink/Seq phenotype file into
                        a matrix of binary sample properties.
plotAllChromosomeValues
                        Plot to a png file the values for the given
                        intervals.
plot_XHMM_genes         Plot the XHMM CNV spanning the input genes.
plot_XHMM_region        Plot the XHMM CNV spanning the input region.
plot_XHMM_targets       Plot the XHMM CNV spanning the input target
                        indices.
readNamedMatrix         Quickly read a rectangular matrix that has row
                        and column names.
readPedigreeFile        Read a Plink/Seq pedinfo file.
readPhenotypesFile      Read a Plink/Seq phenotype file.
scanVectorMayNotExist   Read in an unnamed vector.
sourceDir               Run source across the entire set of specified
                        files in a given directory.
targetsToChrBp1Bp2      Parse a list of genomic intervals into their
                        component chromosome, start, and stop.
targetsToSizes          Parse a list of genomic intervals into their
                        corresponding span lengths.
xhmmScripts-package     Examine and plot XHMM
                        whole-exome-sequencing-based CNV calls
