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| == 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 == |
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− | #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
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| + | 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!) |
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| + | 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. |
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| + | If you include a sample size column in the result file, it will be used to control the size of each plotted marker. |
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| + | == Customizing the Display of Your Results == |
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| + | All options listed in the Main Table above are available, as well as the options listed below |
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| {| class="wikitable" border="0" cellpadding="3" | | {| class="wikitable" border="0" cellpadding="3" |