fitPolyTools: fitPolyTools: a package with functions related to package...

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

fitPolyTools: a package with functions related to package fitPoly

Description

Package fitPolyTools offers some functions for preparing and selecting input data for package fitPoly, and for inspection and analysis of polyploid dosage calls as produced by fitPoly. These analyses focus on the segregation of dosages in an F1 progeny of two parents. The functions can be grouped as follows:

data preparation functions

Functions readFullDataTable and readAxiomSummary convert files generated by Illumina's GenomeStudio and Affymetrix Power Tools software to the input format for fitPoly::fitPoly and fitPoly::fitMarkers.

data visualization functions

Functions XYplot and drawXYplots draw scatterplots of the samples for one marker at a time, possibly with colors indicating the assigned dosages and/or highlighting specific samples. Function combineFiles combines X and Y columns from one file or data.frame with column geno from another.

segregation type functions

The functions calcSegtypeInfo, selSegtypeInfo and segtypeInfoSummary produce information on the possible F1 segregation types. These functions are primarily developed for use in other functions but are also available for users.

identification of the probable segregation types

Function checkF1 gives for all markers the most likely (best fitting) segregation type, based on the F1 and the parental samples. Function correctDosages checks for possibly "shifted" markers (e.g. all dosages scored one lower or higher than the true dosage). Function checkF1 can apply shifts when specified.

combining data from two probes for the same SNP

On Affymetrix Axiom SNP arrays it is possible to have the same SNP interrogated from both sides by two different probes. Function compareProbes compares the results from both probes and produces a new, merged marker if they are sufficiently similar. It also writes the results to a data file suitable for linkage mapping functions (package polymapR).
Function removeRedundant takes the result of compareProbes; if a merged marker is present it removes the corresponding separate probe markers.

producing a data file for mapping

Function writeDosagefile produces a data file suitable for linkage mapping functions (package polymapR). This data file has the same format as that produced by compareProbes and removeRedundant (see previous section).
Function F1Dosages2Matrix reads such a dosages file and returns a matrix in the format required by the polymapR package.

reformatting of fitPoly scores file

Function scores2wide reformats the scores file produced by the fitMarkers function of the fitPoly package to "wide" format.

recovery functions

Functions getBatchfiles and concatbatch allow to recover results from already processed batches of markers, in case fitMarkers crashes.

general tools

These tools may be useful by themselves and are therefore made available too. They include leftstr and rightstr: two functions that return substrings from the left or right side, and function checkFilename which tests if a file with the name can be created. Functions readDatfile and writeDatfile are wrappers for read.table and write.table with different default options, suitable for the file formats expected or produced by functions in this package oand fitPoly.

fitPoly documentation built on April 3, 2025, 8:58 p.m.