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Line 22: − 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!) − + + + + + + + + Line 150:
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Make deprecation warning more visible.
=== Uploading Your Association Study Results ===
=== Uploading Your Association Study Results ===
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. When displaying linkage disequilibrium, plotting will be very fast for small windows when HapMap CEU linkage disequilibrium is requested (because pairwise coefficients have been precomputed) and will be a bit slower for larger windows (because linkage disequilibrium coefficients must be computed on the fly).
<span style="color:red">'''The instructions below refer to a "legacy" service that is not actively maintained. For modern datasets, consider using our new [https://my.locuszoom.org my.locuszoom.org] service for the latest features, including manhattan plots and support for build GRCh38.'''</span>
'''Please note: You CAN plot SNPs without rsid using chr6:20122013 format.'''
Association results can be uploaded to our web server using the [http://locuszoom.org/ 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, but can be in chr:pos format), name a gene of interest or provide appropriate genome coordinates. When displaying linkage disequilibrium, plotting will be very fast for small windows when HapMap CEU linkage disequilibrium is requested (because pairwise coefficients have been precomputed) and will be a bit slower for larger windows (because linkage disequilibrium coefficients must be computed on the fly).
If you include a sample size column in the result file, it will be used to control the size of each plotted marker.
If you include a sample size column in the result file, it will be used to control the size of each plotted marker.
| Reference Population for LD
| Reference Population for LD
| n/a
| n/a
| This option allows the user to specify which reference panel is used to obtain LD estimates. The default is CEU from HapMap Phase II but users may select YRI or JPT+CHB from HapMap Phase II, or CEU from 1000 Genomes (August 2009 release).
| This option allows the user to specify which reference panel is used to obtain LD estimates. The default is CEU from HapMap Phase II but users may select YRI or JPT+CHB from HapMap Phase II, or CEU from 1000 Genomes (August 2009 or June 2010 release).
|-
|-
| Highlight Region of Interest
| Highlight Region of Interest
