glossary.html

VALID: Visualization of Association and Linkage Disequilibrium

Data file to upload: Enter the name and location of the file you would like to upload for display here or browse to find your file by clicking the “browse” button. A default file from Haiman et al. is provided when no file is uploaded.
HapMap population: Enter the appropriate HapMap population for your data.
Chromosome: Enter the chromosome number that corresponds to the uploaded data.
Starting SNP rs#: Enter the reference SNP (rs) number of the first SNP to be displayed. The program will automatically select the first SNP in the uploaded data as a default unless a specific SNP is selected.
Number of SNPs forward: Enter the number of SNPs to display. Default is set to 160.

Results plotted: Results can be plotted on a Χ2 scale or -log10(p-value) scale. Default is “-log10(p-value)”.
Smoothing: Results can be shown in smoothed (convolved with a 7x7 linear kernel) or raw form. Default is smoothing “on”.
SNP annotation position: SNP labels can be displayed to the left or right of the image. Default is “right.”
Annotate all SNPs: Enter “yes” to display all SNPs rs numbers or “no” to display only the SNPs that are likely sources of association signals. Default is “no.”
Annotation threshold: This option allows users to change the significance threshold that must be reached to display a SNP label. Lowering the number will increase the number of SNPs displayed, and conversely increasing the number will decrease the number of SNPs to be displayed. Default is set to max Χ2 / 1.5.
Grid size: Select the size of the color density plot. Default is “auto,” which creates a plot that fits within a standard size web page.
Number of colors: Select the number of colors that are displayed on the color density plot. Default is “253.”
Color Palette: Select the color palette used for the color density plot. Default is a palette drawn from the GOLD program, biased for small values.