CodomMarker             Function to fit a multiple mixture model to a
                        vector of signal ratios of a single bi-allelic
                        marker
F1Dosages2Matrix        Convert the F1 dosage scores data.frame or file
                        to polymapR input matrix
XY_plot                 Draws an XY-plot showing allele signals and
                        assigned dosages
XYdat                   A data set containing SNP array data
calcRstats              Calculate statistics of R per marker
calcSegtypeInfo         Build a list of segregation types
checkF1                 Identify the best-fitting F1 segregation types
checkFilename           Check if a file can be created
combineFiles            Combine the X and Y intensity scores and the
                        assigned dosage in one file
compareProbes           Compare and combine results from two probes for
                        the same SNP
concatbatch             Construct the log, models and scores files from
                        a set of batch files
convertStartmeans       A function to convert a set of mixture means
                        from one ploidy to another
correctDosages          Check if dosage scores may have to be shifted
drawXYplots             Draws a series of pages, each with 6 XY-plots
                        showing allele signals and assigned dosages
expandUnknownParents    Generate markers with all combinations of
                        parental scores
fitMarkers              Function to fit mixture models for series of
                        markers and save the results to files
fitOneMarker            Function to fit multiple mixture models to
                        signal ratios of a single bi-allelic marker
fitPoly                 fitPoly: a package for assigning dosage scores
                        based on SNP array data
fitPolyTools            fitPolyTools: a package with functions related
                        to package fitPoly
fitPoly_data            Small fitPoly input datasets for testing and
                        examples
get.genocol             Generate a set of genotype (dosage) colors for
                        XY-plots
getBatchFiles           get the names of all batch files present
leftstr                 Get substrings from the lefthand side
listSegtypes            conversion of segtype code to F1 segregation
                        ratios
makeFitPolyFiles        Make input files for fitPoly containing only
                        selected rows and columns
readAxiomSummary        convert an Affymetrix AxiomCT1.summary file to
                        the import format for fitPoly
readDatfile             User-friendly wrapper for read.table
readFullDataTable       convert a GenomeStudio FullDataTable file to
                        the import format for fitPoly
removeRedundant         Remove redundant single-probe markers
rightstr                Get substrings from the righthand side
samplestats             Statistics for each F1 sample over all markers
saveMarkerModels        DEPRECATED: Function to fit mixture models for
                        series of markers and save the results to files
scores                  A data set with dosage scores generated by
                        fitPoly
scores2wide             Convert a scores file from long to wide format
segtypeInfoSummary      Summarize the segtypeInfo list
selMarkers_byR          Select markers at specified R levels
selMarkers_qall         Sample markers at several qall levels
selSegtypeInfo          Restrict a list of segregation types to
                        specified inheritance modes
splitNrenameSamples     Rename samples from array codes to user codes,
                        and split diploid from polyploid samples
writeDatfile            User-friendly wrapper for write.table
writeDosagefile         Write a file with segregation types and dosage
                        scores
