| 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 |
| CodomMarker | Function to fit a multiple mixture model to a vector of... |
| combineFiles | Combine the X and Y intensity scores and the assigned dosage... |
| compareProbes | Compare and combine results from two probes for the same SNP |
| concatbatch | Construct the log, models and scores files from a set of... |
| convertStartmeans | A function to convert a set of mixture means from one ploidy... |
| correctDosages | Check if dosage scores may have to be shifted |
| drawXYplots | Draws a series of pages, each with 6 XY-plots showing allele... |
| expandUnknownParents | Generate markers with all combinations of parental scores |
| F1Dosages2Matrix | Convert the F1 dosage scores data.frame or file to polymapR... |
| fitMarkers | Function to fit mixture models for series of markers and save... |
| fitOneMarker | Function to fit multiple mixture models to signal ratios of a... |
| fitPoly | fitPoly: a package for assigning dosage scores based on SNP... |
| fitPoly_data | Small fitPoly input datasets for testing and examples |
| fitPolyTools | fitPolyTools: a package with functions related to package... |
| getBatchFiles | get the names of all batch files present |
| get.genocol | Generate a set of genotype (dosage) colors for XY-plots |
| 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... |
| readAxiomSummary | convert an Affymetrix AxiomCT1.summary file to the import... |
| readDatfile | User-friendly wrapper for read.table |
| readFullDataTable | convert a GenomeStudio FullDataTable file to the import... |
| 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... |
| 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... |
| splitNrenameSamples | Rename samples from array codes to user codes, and split... |
| writeDatfile | User-friendly wrapper for write.table |
| writeDosagefile | Write a file with segregation types and dosage scores |
| XYdat | A data set containing SNP array data |
| XY_plot | Draws an XY-plot showing allele signals and assigned dosages |
