Bioconductor Quantsmooth Sex Chromosome Error

Question

[Perry]

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?

[Paulo Nuin]

I don't know about your error, but why not use Circos to generate plots?

Answer 1

[Jan Oosting]

Hi Perry,

The newest (development) version of quantsmooth has already solved this issue.

You can just use the prepareGenomePlot() function of that version together with the current version of quantsmooth, or use the development version of the package in the current version of R

Answer 2

[Nikol]

I have the exact same problem, using the newest version of the package. The X chromosome coordinates appear somewhere on the lower left corner as an unrelated dot to the ideogram, never in the right position. Any suggestions?

Answer 3

[Jessica]

I too am having this problem. I have updated my version of quantsmooth as recommended but still have the problem. Has anyone come up with a solution yet?