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= LocusZoom =
= LocusZoom =
[[Category:Software]]
[[Image:LocusZoomSmall.png]]
'''LocusZoom''' is designed to facilitate viewing of local association results together with useful information about a locus, such as the location and orientation of the genes it includes, linkage disequilibrium coefficients and local estimates of recombination rates. It was developed by popular demand, as a result of many questions we have had about "How did you make the figures in your talk?" or "How did you make the figures for your GWAS paper?" (And for better or for worse, we have quite a few GWAS papers!!).
LocusZoom can be used in three ways:
; Plot Summaries of Your Genomewide Scan Interactively
: You can upload summary results of your own genomewide scan or genomewide meta-analysis and request plots of regions of interest using a web-based form.
; Generate Many Plots in Batch Mode
: You can upload summary results for your genomewide scan or genomewide meta-analysis and request several plots in one go by uploading a batch file. You will receive results via e-mail. A snail-mail option is not available.
; Plot Summaries of Publicly Available Datasets
: Currently, this includes the results of [http://www.sph.umich.edu/csg/abecasis/public/lipids2008/ our genome-wide scan] for variants associated with HDL-cholesterol, LDL-cholesterol and triglyceride levels in ~20,000 individuals.
We are also developing a distributable code package that you can install on your own system to generate plots locally. This is not yet available, but is expected in April 2010.
== Generate single plots using our publicly-available lipids GWAS data ==
== Generate single plots using our publicly-available lipids GWAS data ==
{| class="wikitable" border="0" cellpadding="3"
{| class="wikitable" border="0" cellpadding="3"
|- bgcolor="lightgray"
|- bgcolor="lightgray"
! Setting
! Setting
! Default Value
! Default Value
! Details
! Details
|-
|-
|}
|}
== Uploading your own file and use the batch mode ==
== Uploading your own file and use the batch mode ==
Example of a specification file (must include a header);
#Uploading a file<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.
<pre>
#Uploading the specification file<br>Users can upload a specification file which allows for the easy generation of dozens of plots, where each plot can be customized for even more features than available on the web interface for LocusZoom. The file is required to have 7 white space-delimited columns, where the last column can be blank. The header is not important, but LocusZoom expects a header to exist. To define a region to plot, users may specify either i) a SNP name in the first column and the appropriate flanking region (e.g. 200kb, 500kb, 1Mb) in the fifth column, or ii) a gene name in the first column and the appropriate flanking region in the fifth column, or iii) a chromosome number, start and stop positions in the 2nd, 3rd and 4th columns respectively. If option ii) is selected, LocusZoom will select the most significant SNP in the region as the index SNP. If option iii) is chosen, the index SNP for the plot must be specified in the first column. For distances <= 500kb where the lead SNP is a HapMap SNP and LD from CEU is requested, the plots will be generated very quickly because we have pre-computed LD for all HapMap SNPs in the CEU. The sixth column is used to select which regions should be plotted. For example, if you run a specification file with 15 plots and 14 of them turn out very nicely, you may wish to re-run the specification file with some modifications to a single row of the specification file to tweak the last remaining plot. In this case, you could change the 14 plots you don’t need to re-run to “no” under the 6th column (“run” column) and leave the 15th plot you’d like to re-run as “yes” in this column. The 7th and final column contains optional LocusZoom arguments (see the 2nd column of Table 1.3 above). As many options as the user wishes to change can be specified in 7th column and LocusZoom options should be separated by spaces.
specfile.txt
Example of a specification file (must include a header);
<pre>specfile.txt
snp chr start end flank run m2zargs
snp chr start end flank run m2zargs
rs1 NA NA NA 500kb yes rfrows=3 weightCol=”N” snpset=”HapMap” metalRug=”Our SNPs”
rs1 NA NA NA 500kb yes rfrows=3 weightCol=”N” snpset=”HapMap” metalRug=”Our SNPs”
rs2 1 540000 580000 NA yes rfrows=4 legend=”right” showAnnot=T
rs2 1 540000 580000 NA yes rfrows=4 legend=”right” showAnnot=T
CETP NA NA NA 200kb yes rfrows=6 showAnnot=T annotPch=”1,24,24,25,22,21,8,7”</pre>
CETP NA NA NA 200kb yes rfrows=6 showAnnot=T annotPch=”1,24,24,25,22,21,8,7”</pre>
[[Category:Software]]
