Changes

== Upload your own meta-analysis file and generate single plots using a web-based form  ==

== Upload your own meta-analysis file and generate single plots using a web-based form  ==

#Uploading your own association results<br>Association results can be uploaded to our web server using the LocusZoom webpage, which will accept a typical meta-analysis file for ~2.5 million SNPs provided the user selects only the required columns (SNP Name, p-value, and optionally, N) and gzips the file before uploading. In our tests, this results in a file ~17 Mb which is below the 20 Mb file size limit. This allows users to draw multiple plots from the LocusZoom website while only uploading the meta-analysis results file one time. Alternatively, for faster viewing of a single region, users can upload a file that contains only the rows corresponding to SNPs in the region of interest or a particular chromosome. Users need to specify the name of the column containing SNP identifiers (rs numbers or genome-based names such as chr1:400000 where the position is from the same build as that being plotted, typically hg18) and the name of the column containing p-values. Data points can optionally be sized according to the square-root of user-specified weights such as sample size. Providing the name of the weight column turns this feature on.

=== Uploading Your Association Study Results ===

#Options specific to uploading your own results<br>All options listed in 1.3 above are available, as well as the options listed below

 

Association results can be uploaded to our web server using the [http://csg.sph.umich.edu/locuszoom/ plot your data webpage]. Result files are limited to 20Mb in size, which allows for a [[gzip|gzipped]] text table including key columns (marker name, p-value and sample size) for up to ~3 million SNPs. In our tests, a typical GWAS results file is ~17 Mb in size after imputation of HapMap SNPs. Once a file is uploaded, LocusZoom will remember the file for the duration of your web session allowing you to generate multiple plots. If you have a slow connection or would like to save time, you can upload results for a region or chromosome of interest only. Your results are entirely confidential and won't be viewed by us or anyone else (except those with whom you share them!)

 

To specify the region to be plotted, you will have to specify the name of a key marker in the region (typically, as an rs-number), name a gene of interest or provide appropriate genome coordinates.

 

If you include a sample size column in the result file, it will be used to control the size of each plotted marker.

 

== Customizing the Display of Your Results ==

 

All options listed in the Main Table above are available, as well as the options listed below

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