makeFitPolyFiles: Make input files for fitPoly containing only selected rows...

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Make input files for fitPoly containing only selected rows and columns

Description

Remove entire markers and ratios for samples within markers from fitPoly inputfiles if their R levels are below some thresholds; also keep only the MarkerName, SampleName, X, Y, R and ratio columns

Usage

makeFitPolyFiles(datpoly, datdiplo=NA, out,
filetype=c("dat", "RData")[2], Rquantile=0.95, marker.threshold,
Rthreshold.param=c(0.95, 0.5, 0))

Arguments

datpoly	data.frame as produced by readFullDataTable, readAxiomSummary or splitNrenameSamples, with at least columns MarkerName, SampleName, R and ratio
datdiplo	data.frame as produced by splitNrenameSamples, with at least columns MarkerName, SampleName, R and ratio, containing the data for the diploid samples; or NA (default)
out	output files will be named out + _poly.RData and _diplo.RData (or .dat if filetype is set to "dat"). If NA no files are written
filetype	"RData" (default) or "dat": the format to save the data in
Rquantile	a value between 0 and 1: the R (= X + Y) quantile on which selection of markers is based
marker.threshold	the minimum value of the Rquantile for a marker to be selected
Rthreshold.param	a vector of length 3, defining an R threshold for selecting samples within each marker. The first number is the R quantile, the second is a number to multiply that R quantile with, and the third is the minimum value of the result. The default of c(0.95, 0.5, 0) means that 0.5 * the 95 (which is always higher than 0, the minimum result). This is often a good cut-off value to discard samples within a marker.

Details

All rows for markers not meeting the marker.threshold for the R quantile are removed from the original data.frames. For samples within the remaining markers where the R value is below the marker-specific threshold the ratio is set to NA, the row for that sample is not removed. The same thresholds are applied to datpoly and datdiplo.

Value

a list with two elements: datpoly is a filtered version of parameter datpoly, and if param datdiplo was specified the second element of the returned list is datdiplo: a filtered version of parameter datdiplo. Either or both may have 0 rows left after filtering. If no datdiplo was specified the second element of the list is NA.
If parameter out is specified the element(s) of this list are also saved as files.

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