selMarkers_byR: Select markers at specified R levels

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Select markers at specified R levels

Description

Select markers based on their R statistics, for studying the relation between R level and marker quality

Usage

selMarkers_byR(Rstats, Rlevels, mrkperlevel=1, stat="q95")

Arguments

Rstats	a data frame as returned by calcRstats
Rlevels	a vector of R levels in increasing order (preferably from the minimum to the maximum of stat over all markers in Rstats)
mrkperlevel	number, default 1: the number of markers to select at each of the levels in Rlevels
stat	the name of one of the statistics columns in Rstats

Details

The return value of this function is intended to be used for studying the relation between the marker quality and the value of the chosen R statistic, e.g. by drawing XY-plots of each of the selected markers. By finding a suitable threshold for the R statistic bas markers could be excluded from evaluation by fitPoly, saving time because bad markers take the longest to be scored and are then often rejected anyway.

Value

a selection from Rstats, in ascending order of column stat. The first <mrkperlevel> markers with stat above each Rlevel are returned; duplicated selections are removed (so the number of returned markers may be less than length(Rlevels) * mrkperlevel)

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