R: Genotype Calling for Bi-Allelic Marker Assays

# Genotype Calling for Bi-Allelic Marker Assays

## Documentation for package ‘fitPoly’ version 4.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

fitPoly-package | fitPoly: a package for assigning dosage scores based on 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
CodomMarker | Function to fit a multiple mixture model to a vector of signal ratios of a single bi-allelic marker
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
F1Dosages2Matrix | Convert the F1 dosage scores data.frame or file to polymapR input matrix
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
XYdat | A data set containing SNP array data
XY_plot | Draws an XY-plot showing allele signals and assigned dosages