Changes

: 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:

: 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:

<quote>

<source>

Feature    chr    start    end      flank        plot    arguments

Feature    chr    start    end      flank        plot    arguments

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”  

</quote>

</source>

; Plotting a region flanking an interesting SNP

; Plotting a region flanking an interesting SNP

: 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:

: 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:

<code>

<source>

Feature    chr    start    end      flank        plot    arguments

Feature    chr    start    end      flank        plot    arguments

rs2     1     540000  580000  na     yes      rfrows=4 legend=”right” showAnnot=T  

rs2     1     540000  580000  na     yes      rfrows=4 legend=”right” showAnnot=T  

</code>

</source>

; Plotting a region flanking a gene of interest

; Plotting a region flanking a gene of interest

: 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:

: 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:

<code>

<source>

Feature    chr    start    end      flank        plot    arguments

Feature    chr    start    end      flank        plot    arguments

CETP     na     na       na      200kb        yes      rfrows=6 showAnnot=T annotPch=”1,24,24,25,22,21,8,7”

CETP     na     na       na      200kb        yes      rfrows=6 showAnnot=T annotPch=”1,24,24,25,22,21,8,7”

</code>

</source>

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”.

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”.