[#1817] problem when adding snp-subset to existing manhattanplot with add.plot(snp.subset(), ... )

Date:
2012-02-13 15:48 Priority:
3

State:
Open

Submitted by:
Benedikt Haug (arabidopsis) Assigned to:
Nobody (None)

Resolution:
Awaiting Response Operating System:
All

Severity:
normal Hardware:
All

Version:
v1.7-0 Component:
GenABEL

URL:

Summary:
problem when adding snp-subset to existing manhattanplot with add.plot(snp.subset(), ... )

Detailed description
Setup: 1) I generate a full data (=whole genome) Manhattan plot 2) I want to add a snp subset in another color to the existing plot to highlight certain SNPs/areas, using add.plot(snp.subset(x,subset), col=...) 3) Result: added points appear as desired on chromosome 1, aligning perfectly with existing points. However, added points do not match on other chromosomes (option delta was set to an equal value in both, plot() and add.plot() ). Interestingly, the points perfectly align when datasets of same sizes are utilised. (Plotting full data over full data, plotting subset over subset). Another observation is, that if the subset does not contain SNPs from Chromosome 1, other SNPs are plotted on chromosome one. Help needed, since this would be an extremely handy way to highlight candidate genes/regions in a Manhattanplot and therefore to provide a very intuitive way to access analysis results! Cheers, Ben.

Comments:

Message
Date: 2013-06-07 07:41 Sender: Lennart Karssen Apologies for waiting so long with following up on this bug. I tried to replicate this bug in GenABEL v1.7-6, but it doesn't seem to be a problem (anymore). Could you verify this? Please see the attached script for the tests that I ran.
Date: 2012-02-21 14:49 Sender: Benedikt Haug Hey, thanks for taking notice of the issue. I am using GenABEL v. 1.7-0.
Date: 2012-02-21 13:22 Sender: Lennart Karssen Thanks for reporting this issue as well as for the follow up. Could you tell us which version of GenABEL you are using?
Date: 2012-02-20 21:45 Sender: Benedikt Haug Additional info: By coloring the subset in a way like this... add.plot(snp.subset(gwas.FT.ibs, snpsubset=unionframes), col=rep(colors()[c(552,255,456)])) ... the subset seems to get colored chromosomewise. By that I understood that the combination of add.plot(snp.subset(data,snpsupset)) does not take into account the snp positions of the previous (in my case full genome) plot(data) but just 'pastes' the subset together where chromosomes end (instead of inserting an appropriate spacer here). This is clearly visible as the first SNP of Chr2 (of the subset) is plotted upon the last snp of Chr1 (of the subset), the first of Chr3(...) upon the last of Chr 2(...) and so forth, leading to an increasing misalignment with the existing Manhattanplot with increasing chromosome number. This is surprising, since as I wrote, on Chromosome one SNPs perfectly align, so that here a correct spacer seems to get inserted at the beginning (left of the first snp of the subset).

Attached Files:

Attachments:

Size	Name	Date	By	Download
991 bytes	GA-GWAS.R	2013-06-07 07:41	lckarssen	GA-GWAS.R

Changes

Field	Old Value	Date	By
Resolution	None	2013-06-07 07:41	lckarssen
Operating System	None	2013-06-07 07:41	lckarssen
Severity	None	2013-06-07 07:41	lckarssen
Hardware	None	2013-06-07 07:41	lckarssen
File Added	622: GA-GWAS.R	2013-06-07 07:41	lckarssen
Version	None	2012-02-21 15:02	lckarssen
Component	None	2012-02-21 13:22	lckarssen