selMarkers_byR {fitPoly} | R Documentation |
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)