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