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Jump to navigationJump to search→Generate single plots using our publicly-available lipids GWAS data
| Human Genome Build || n/a (must be selected from web form) || Plots can be generated based on hg 18 (default) or hg17 positions
| Human Genome Build || n/a (must be selected from web form) || Plots can be generated based on hg 18 (default) or hg17 positions
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| Legend Location || legend=”right” || This specifies the location of the legend within the plot, the default is left
| Legend Location || legend=”left” || This specifies the location of the legend within the plot, the default is auto. Auto tries to select the preferential location (either left or right) depending on the location of data points.
(left, right, none)
(auto, left, right, none)
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| Show RUG || snpset=”HapMap”<br>To display rug for SNPs in analysis file;<br>metalRug=”Rug SNPs” || Show a “rug” at the top of the plot – a series of vertical tick marks highlighting the positions of SNPs from HapMap CEU (here given as “HapMap”) or the markers shown in the plot (use metalRug)
| Show RUG || snpset=”HapMap”<br>To display rug for SNPs in analysis file;<br>metalRug=”Rug SNPs” || Show a “rug” at the top of the plot – a series of vertical tick marks highlighting the positions of SNPs from HapMap CEU (here given as “HapMap”) or the markers shown in the plot (use metalRug)
| LD Measure || ldCol=”dprime” (“rsquare”) || The color of the data points reflects the LD (r2) with the index SNP.
| LD Measure || ldCol=”dprime” (“rsquare”) || The color of the data points reflects the LD (r2) with the index SNP.
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| HapMap Population for LD || n/a (must be selected from web form) || This option allows the user to specify which HapMap population was used to obtain LD estimates. The default is CEU but users may select YRI or JPT+CHB
| HapMap Population for LD || n/a (must be selected from web form) || This option allows the user to specify which population is used to obtain LD estimates. The default is CEU from HapMap Phase II but users may select YRI or JPT+CHB from HapMap Phase II, or CEU from 1000 Genomes (August 2009 release).
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| Highlight Region of Interest || hiStart=425Mb<br>hiEnd=425.1Mb || A grey box can be used to highlight important regions of the genome – this can reflect the region of an association signal or a region being sequenced, etc.
| Highlight Region of Interest || hiStart=425Mb<br>hiEnd=425.1Mb || A grey box can be used to highlight important regions of the genome – this can reflect the region of an association signal or a region being sequenced, etc.
