Changes

# Upload your own meta-analysis file and generate many plots at once by uploading a specification file.  Results will be emailed back to the user.

# Upload your own meta-analysis file and generate many plots at once by uploading a specification file.  Results will be emailed back to the user.

== Generate single plots using our publicly-available lipids GWAS data ==

== Generate single plots using our publicly-available lipids GWAS data ==

Table 1.3 Additional options available from the web form

#Selecting regions to display using our lipids data<br>The plots were designed to examine ~ 1 Megabase windows of the genome, although for regions with several association signals or long-range linkage disequilibrium patterns, plots extending as large as a few Mb can be drawn. The user can specify the region to display in the LocusZoom plot in one of three ways; 1) an index SNP and a flanking region, 2) the chromosome together with start and stop positions (in basepairs), 3) gene name and a flanking region.

#Displaying LD information<br>In the main plot window, data points are colored according to their level of linkage disequilibrium (LD) with the index SNP. If users specify the region to display using an index SNP and flanking region, LD of all data points will be relative to the user-specified index SNP. If users specify the region to display using options 2 and 3 above, LocusZoom will select the most significant SNP in the region. For all other SNPs in the plot, the color of the data point will reflect the pair-wise LD patterns with this index SNP. The default LD which will be displayed is r2 from the HapMap CEU population (release 22), but users have the option to select either r2 or D’ from; HapMap CEU, HapMap YRI, Hapmap CHB+JPT, 1000 Genomes CEU. Because we have pre-computed LD for all SNPs in HapMap CEU, plots will generate very quickly if using the default LD information, provided the region to display is less than 500kb either side of the index SNP. SNPs with missing LD information are shown in grey.

{| border="1" padding="2" width="80%"

 

{| border="1" width="80%" align="center"

|- bgcolor="lightgray"

|- bgcolor="lightgray"

! Web Form Option

! Web Form Option  

! Batch Mode Command File Option

! Batch Mode Command File Option  

! Description

! Description

|-

|-

| Title on Plot || title=”My Favorite Locus” || The title above the plot can be specified

| Title on Plot  

| title=”My Favorite Locus”  

| The title above the plot can be specified

|-

|-

| 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

|-

|-

| 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.

| Legend Location  

(auto, left, right, none)

| 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.  

(auto, left, right, none)  

 

|-

|-

| Maximum Rows of Gene Names || rfrows=4 || LocusZoom will automatically determine the optimal number of rows to display genes and gene names so they are not overlapping.  However, if the user wishes to keep all plots the same size, the maximum number of gene rows can be specified.  Additional genes may be left off the figure to accommodate this feature so please use with caution. If genes are missing from the plot, this will be indicated on the plot.

| 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). Remove the rug in batch mode using snpset=NULL. Other options include "Affy500",or "Illu318", or use "Affy500,Illu318,HapMap" to see all 3.

|-

|-

| Point Size Proportional to Sample Size || weightCol=”SampleSize” || This specifies that the “dot size” of the data points will reflect the square-root of the sample size (to reflect the s.e.).  The default is to have all dot sizes remain the same size.

| Maximum Rows of Gene Names

| rfrows=4

| LocusZoom will automatically determine the optimal number of rows to display genes and gene names so they are not overlapping. However, if the user wishes to keep all plots the same size, the maximum number of gene rows can be specified. Additional genes may be left off the figure to accommodate this feature so please use with caution. If genes are missing from the plot, this will be indicated on the plot.

|-

|-

| LD Measure || ldCol=”dprime” (“rsquare”) || The color of the data points reflects the LD (r2) with the index SNP. The default is "rsquare".

| Point Size Proportional to Sample Size

| weightCol=”SampleSize”

| This specifies that the “dot size” of the data points will reflect the square-root of the sample size (to reflect the s.e.). The default is to have all dot sizes remain the same size.

|-

|-

| 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).

| LD Measure

| ldCol=”dprime” (“rsquare”)  

| The color of the data points reflects the LD (r2) with the index SNP. The default is "rsquare".

|-

|-

| 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.

| 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).

|-

|-

| Theme || theme=”publication” || We have created a theme that has larger text and is more easily readable for publication.

| 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.

|-

|-

| Show Annotation || showAnnot=T<br>showRefsnpAnnot=T<br>annotPch=”21,24,24,25,22,22,8,7” || SNP annotation is available for all 1000G SNPs (Aug 2009 release) and can be displayed on the plot using this option.  On the website, various annotation options can be turned on or off.<br>Certain annotation fields can be turned on or off using the annotPch command.  To show several categories of SNPs as the same symbol, simply give the same R symbol code for those categories (e.g. annotPch=”21,24,24,25,22,22,8,7”).  The category listings, together with their default symbol setting are;<br>Framestop (24, triangle)<br>Splice (24, triangle)<br>NonSynonymous (25, inverted triangle)<br>Synonymous (22, square)<br>UTR (22, square)<br>TFBScons (8, star)<br>MCS44 Placental (7, square with diagonal lines)<br>None-of-the-above (21,  filled circle).  <br>For more information about the annotation categories used, please see http://research.nhgri.nih.gov/tools/unisnp/?rm=ohelp

| Theme

| theme=”publication”

| We have created a theme that has larger text and is more easily readable for publication.

|-

|-

| Recombination Rate Overlay || showRecomb=T || The estimated recombination rate from HapMap samples can be shown on the plot, or left off. The data plotted are from Hapmap; http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/2008-03_rel22_B36/rates/

| Show Annotation

| showAnnot=T<br>showRefsnpAnnot=T<br>annotPch=”21,24,24,25,22,22,8,7”

| SNP annotation is available for all 1000G SNPs (Aug 2009 release) and can be displayed on the plot using this option. On the website, various annotation options can be turned on or off.<br>Certain annotation fields can be turned on or off using the annotPch command. To show several categories of SNPs as the same symbol, simply give the same R symbol code for those categories (e.g. annotPch=”21,24,24,25,22,22,8,7”). The category listings, together with their default symbol setting are;<br>Framestop (24, triangle)<br>Splice (24, triangle)<br>NonSynonymous (25, inverted triangle)<br>Synonymous (22, square)<br>UTR (22, square)<br>TFBScons (8, star)<br>MCS44 Placental (7, square with diagonal lines)<br>None-of-the-above (21, filled circle). <br>For more information about the annotation categories used, please see http://research.nhgri.nih.gov/tools/unisnp/?rm=ohelp

|-

|-

|}

|}