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LocusZoom (view source)

Revision as of 09:10, 15 April 2010

875 bytes added ,  09:10, 15 April 2010
→‎Generating a Hit Spec File
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=== Generating a Hit Spec File ===
 
=== Generating a Hit Spec File ===
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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.
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Batch mode allows you to conveniently specify a set of plots to be generated in "Hit Spec" file. This is handy if you need to generate large numbers of plots or if you want to plot the same set of regions after updating a genomewide analysis (for example).
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Example of a specification file (must include a header);
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The "Hit Spec" file is a whitespace delimited text file. The file has six mandatory columns which can be followed by a series of optional '''key'''=''value'' pairs to allow for detailed customization of each plot. The first line in the file is assumed to be a header and is ignored. Each subsequent line describes a single plot. There are three ways to select a region to plot:
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  <-- Contents of specfile.txt -->
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; Plotting a window flanking an interesting SNP
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   snp   chr    start    end      flank        run     m2zargs
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: This option allows you to plot results for all markers within a specific distance (e.g. 500kb) of an index SNP. To use this option, set column 1 to have the name of the index SNP (e.g. ''rs2'' below) and set column 5 to specify the width of the region of interest (e.g. 500kb below). Here is an example:
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   rs1 NA NA   NA   500kb yes     rfrows=3 weightCol=”N” snpset=”HapMap” metalRug=”Our SNPs”  
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   rs2 1 540000   580000  NA         yes     rfrows=4 legend=”right” showAnnot=T  
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<code>
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   CETP NA NA   NA   200kb yes     rfrows=6 showAnnot=T annotPch=”1,24,24,25,22,21,8,7”
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   Feature   chr    start    end      flank        plot     arguments
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   rs1     na     na       na      500kb       yes     rfrows=3 weightCol=”N” snpset=”HapMap” metalRug=”Our SNPs”  
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</code>
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; Plotting a region flanking an interesting SNP
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: This option is similar to the previous option, but allows you to specify an assymetric region of interest. For example, perhaps you interested in a plot that extends a bit further to the right of the SNP of interest. In this case, specify the coordinates of the region to be plotted in columns 2, 3, and 4. Here is an example:
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<code>
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  Feature    chr    start    end      flank        plot    arguments
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   rs2     1     540000  580000  na     yes     rfrows=4 legend=”right” showAnnot=T  
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</code>
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; Plotting a region flanking a gene of interest
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: This option allows you to focus on a particular gene, rather than a specific SNP. It is similar to the first option. You should set column 1 to be the name of the gene of interest and column 5 to be the desired window width. When you use this option, LocusZoom will automatically select an index SNP for each region; the SNP will be the site with the smallest p-value. Here is an example:
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<code>
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  Feature    chr    start    end      flank        plot    arguments
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   CETP     na     na       na      200kb       yes     rfrows=6 showAnnot=T annotPch=”1,24,24,25,22,21,8,7”
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</code>
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The sixth column in the "Hit Spec" file can be used to enable (with the value ''yes'') or disable (with the value ''no'') an individual plot. For example, if you run a "Hit Spec" file with 15 plots and 14 of them turn out very nicely, you may wish to re-run the "Hit Spec" file with some tweaks to the problem plot. In this case (if you dislike waiting for your results as much as we do!), you could disable generation of the plots that seem nice by changing the 6th column to “no” and leave the plot that you tweaked as a “yes”.
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The 7th and final column contains additional LocusZoom arguments as '''key'''=''value'' pairs. Any number of '''key'''=''value'' pair arguments can be included. For details of available options, see the section entitled LocusZoom options below.
    
== Generate single plots using our publicly-available lipids GWAS data  ==
 
== Generate single plots using our publicly-available lipids GWAS data  ==
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/1128"

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