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== Upload your own meta-analysis file and generate single plots using a web-based form ==
== Upload your own meta-analysis file and generate single plots using a web-based form ==
#Uploading your own association results<br>Association results can be uploaded to our web server using the LocusZoom webpage, which will accept a typical meta-analysis file for ~2.5 million SNPs provided the user selects only the required columns (SNP Name, p-value, and optionally, N) and gzips the file before uploading. In our tests, this results in a file ~17 Mb which is below the 20 Mb file size limit. This allows users to draw multiple plots from the LocusZoom website while only uploading the meta-analysis results file one time. Alternatively, for faster viewing of a single region, users can upload a file that contains only the rows corresponding to SNPs in the region of interest or a particular chromosome. Users need to specify the name of the column containing SNP identifiers (rs numbers or genome-based names such as chr1:400000 where the position is from the same build as that being plotted, typically hg18) and the name of the column containing p-values. Data points can optionally be sized according to the square-root of user-specified weights such as sample size. Providing the name of the weight column turns this feature on.
#Uploading your own association results<br>Association results can be uploaded to our web server using the LocusZoom webpage, which will accept a typical meta-analysis file for ~2.5 million SNPs provided the user selects only the required columns (SNP Name, p-value, and optionally, N) and gzips the file before uploading. In our tests, this results in a file ~17 Mb which is below the 20 Mb file size limit. This allows users to draw multiple plots from the LocusZoom website while only uploading the meta-analysis results file one time. Alternatively, for faster viewing of a single region, users can upload a file that contains only the rows corresponding to SNPs in the region of interest or a particular chromosome. Users need to specify the name of the column containing SNP identifiers (rs numbers or genome-based names such as chr1:400000 where the position is from the same build as that being plotted, typically hg18) and the name of the column containing p-values. Data points can optionally be sized according to the square-root of user-specified weights such as sample size. Providing the name of the weight column turns this feature on.
#Options specific to uploading your own results<br>All options listed in 1.3 above are available, as well as the options listed below
#Options specific to uploading your own results<br>All options listed in 1.3 above are available, as well as the options listed below
{| border="1"
{| class="wikitable" border="0" cellpadding="3"
|- bgcolor="lightgray"
! Setting
! Default Value
! Details
|-
|-
| Column Delimiter
| Column Delimiter
| n/a (must be selected from web form)
| none
| Users must specify the type of column delimiter in the results file
| Users must specify the type of column delimiter in the results file
|-
|-
| Pvalue Column Name
| Pvalue Column Name
| n/a (must be selected from web form)
| none
| Users must specify the name of the column that contains the p-values
| Users must specify the name of the column that contains the p-values
|-
|-
| Marker Column Name
| Marker Column Name
| n/a (must be selected from web form)
| none
| Users must specify the heading of the column that contains marker names
| Users must specify the heading of the column that contains marker names
|-
|-
| Human Genome Build
| Human Genome Build
| n/a (must be selected from web form)
| none
| Plots can be generated based on hg18 (default) or hg17 positions
| Plots can be generated based on hg18 (default) or hg17 positions
|-
|-
| HapMap Population for LD
| HapMap Population for LD
| n/a (must be selected from web form)
| none
| 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
| 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
|}
|}
