I'm using quantsmooth to draw chromosome ideograms, but the sex chromosomes are not correctly implemented. According to the documentation, I can use 98 as X and 99 as Y, but this code is not supported by prepareGenomePlot, which translates chromosome locations to plot coordinates. prepareGenomePlot zeros out my data for X and Y points. You can reproduce the problem with the following code and input.

Input file (test_data):

CHR     MapInfo  
1       100
98      100 
12      500

R code:

MapInfo<-read.delim('test_data',header=TRUE,sep='\t')
chrompos<-prepareGenomePlot(MapInfo[,1:2],paintCytobands=TRUE,organism='hsa',sexChromosomes=TRUE)
chrompos

This will show that 98 (X) and the associated MapInfo are forced to 0.

Has anyone run across this error? Before I fix the quantsmooth library, has anyone already remedied this?