-
Notifications
You must be signed in to change notification settings - Fork 24
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
"any data frame" flexibilty needed with gwas data #32
Comments
@vjcitn and @stankiewicz565
Until some hoped-for eventual unification of igvR and igvShiny, I think the best solution is to emulate, in igvShiny, the GWASTrack class API from igvR. There is an inheritance hierarchy to which igvR's GWASTrack belongs. I am reluctant to port all that over right now. Here's a question for you: igvR has both GWASTrack and GWASUrlTrack classes. I favor a single polymorphic class which is smart enough to discern what data (direct or at a url) it is being offered. So I propose to create a simple single GWASTrack for igvShiny (and eventually for igvR also). The data argument in the constructor could be a url or a data.frame. The constructor would test and do the right thing. Regarding the use of/requirement for chrom/pos/pval columns: I follow Jim Robinson on "the GWAS format", though I now understand that this may not be a true standard. I imagine that the table excerpt that you show works because of its use of standard (in some sense) column names. I also once got the impression - I might be wrong- that a common gwas file structure had chromosome in column 12, position in 13, and pvalue in 28. All that seems opaque and tricky - and easily sidestepped by requiring explicit chrom, pos, and pvalue columns to be supplied in all cases. Not burdensome, I don't think. So how about a single GWASTrack S4 class constructor, able to handle both data.frames and urls, requiring explicit chrom/pos/pvalue column numbers? |
Sounds good! |
@vjcitn version 1.5.5 has new S4 class, GWASTrack, just merged into the master branch.
Vince - I'd be glad to test further with a sampling of your GWAS urls. |
Hi @vjcitn. Is there anything that can be done in case of this task? |
@vjcitn - new issue to ease tracking.
emulate these parameters in igvR:
The text was updated successfully, but these errors were encountered: