Question: Bioconductor Quantsmooth Sex Chromosome Error
1
gravatar for Perry
6.7 years ago by
Perry290
philadelphia
Perry290 wrote:

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?

bioconductor • 1.9k views
ADD COMMENTlink modified 6.6 years ago by Jessica0 • written 6.7 years ago by Perry290

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

ADD REPLYlink written 6.7 years ago by Paulo Nuin3.7k
3
gravatar for Jan Oosting
6.6 years ago by
Jan Oosting780
Leiden, NL
Jan Oosting780 wrote:

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

ADD COMMENTlink written 6.6 years ago by Jan Oosting780
0
gravatar for Nikol
6.6 years ago by
Nikol0
Nikol0 wrote:

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?

ADD COMMENTlink written 6.6 years ago by Nikol0
0
gravatar for Jessica
6.4 years ago by
Jessica0
Jessica0 wrote:

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?

ADD COMMENTlink written 6.4 years ago by Jessica0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 935 users visited in the last hour