LocusZoom - Revision history

Abought: Make deprecation warning more visible.

2020-10-28T17:29:06Z

Make deprecation warning more visible.

← Older revision		Revision as of 13:29, 28 October 2020
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	'''The instructions below refer to a "legacy" service that is not actively maintained. For modern datasets, consider using our new [https://my.locuszoom.org my.locuszoom.org] service for the latest features, including manhattan plots and support for build GRCh38.'''		<span style="color:red">'''The instructions below refer to a "legacy" service that is not actively maintained. For modern datasets, consider using our new [https://my.locuszoom.org my.locuszoom.org] service for the latest features, including manhattan plots and support for build GRCh38.'''</span>

Abought: Add deprecation notice and link to new my.locuszoom.org

2020-10-28T17:23:04Z

Add deprecation notice and link to new my.locuszoom.org

← Older revision		Revision as of 13:23, 28 October 2020
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	=== Uploading Your Association Study Results ===		=== Uploading Your Association Study Results ===


			'''The instructions below refer to a "legacy" service that is not actively maintained. For modern datasets, consider using our new [https://my.locuszoom.org my.locuszoom.org] service for the latest features, including manhattan plots and support for build GRCh38.'''


	'''Please note: You CAN plot SNPs without rsid using chr6:20122013 format.'''		'''Please note: You CAN plot SNPs without rsid using chr6:20122013 format.'''

	Association results can be uploaded to our web server using the [http://~~csg.sph.umich~~.~~edu/locuszoom~~/ plot your data webpage]. Result files are limited to 20Mb in size, which allows for a [[gzip\|gzipped]] text table including key columns (marker name, p-value and sample size) for up to ~3 million SNPs. In our tests, a typical GWAS results file is ~17 Mb in size after imputation of HapMap SNPs. Once a file is uploaded, LocusZoom will remember the file for the duration of your web session allowing you to generate multiple plots. If you have a slow connection or would like to save time, you can upload results for a region or chromosome of interest only. Your results are entirely confidential and won't be viewed by us or anyone else (except those with whom you share them!)		Association results can be uploaded to our web server using the [http://locuszoom.org/ plot your data webpage]. Result files are limited to 20Mb in size, which allows for a [[gzip\|gzipped]] text table including key columns (marker name, p-value and sample size) for up to ~3 million SNPs. In our tests, a typical GWAS results file is ~17 Mb in size after imputation of HapMap SNPs. Once a file is uploaded, LocusZoom will remember the file for the duration of your web session allowing you to generate multiple plots. If you have a slow connection or would like to save time, you can upload results for a region or chromosome of interest only. Your results are entirely confidential and won't be viewed by us or anyone else (except those with whom you share them!)

	To specify the region to be plotted, you will have to specify the name of a key marker in the region (typically, as an rs-number, but can be in chr:pos format), name a gene of interest or provide appropriate genome coordinates. When displaying linkage disequilibrium, plotting will be very fast for small windows when HapMap CEU linkage disequilibrium is requested (because pairwise coefficients have been precomputed) and will be a bit slower for larger windows (because linkage disequilibrium coefficients must be computed on the fly).		To specify the region to be plotted, you will have to specify the name of a key marker in the region (typically, as an rs-number, but can be in chr:pos format), name a gene of interest or provide appropriate genome coordinates. When displaying linkage disequilibrium, plotting will be very fast for small windows when HapMap CEU linkage disequilibrium is requested (because pairwise coefficients have been precomputed) and will be a bit slower for larger windows (because linkage disequilibrium coefficients must be computed on the fly).

Cristen: /* Uploading Your Association Study Results */

2013-04-23T15:34:10Z

Uploading Your Association Study Results

← Older revision		Revision as of 11:34, 23 April 2013
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	=== Uploading Your Association Study Results ===		=== Uploading Your Association Study Results ===

			'''Please note: You CAN plot SNPs without rsid using chr6:20122013 format.'''

	Association results can be uploaded to our web server using the [http://csg.sph.umich.edu/locuszoom/ plot your data webpage]. Result files are limited to 20Mb in size, which allows for a [[gzip\|gzipped]] text table including key columns (marker name, p-value and sample size) for up to ~3 million SNPs. In our tests, a typical GWAS results file is ~17 Mb in size after imputation of HapMap SNPs. Once a file is uploaded, LocusZoom will remember the file for the duration of your web session allowing you to generate multiple plots. If you have a slow connection or would like to save time, you can upload results for a region or chromosome of interest only. Your results are entirely confidential and won't be viewed by us or anyone else (except those with whom you share them!)		Association results can be uploaded to our web server using the [http://csg.sph.umich.edu/locuszoom/ plot your data webpage]. Result files are limited to 20Mb in size, which allows for a [[gzip\|gzipped]] text table including key columns (marker name, p-value and sample size) for up to ~3 million SNPs. In our tests, a typical GWAS results file is ~17 Mb in size after imputation of HapMap SNPs. Once a file is uploaded, LocusZoom will remember the file for the duration of your web session allowing you to generate multiple plots. If you have a slow connection or would like to save time, you can upload results for a region or chromosome of interest only. Your results are entirely confidential and won't be viewed by us or anyone else (except those with whom you share them!)

Cristen: /* Uploading Your Association Study Results */

2012-12-11T15:57:55Z

Uploading Your Association Study Results

← Older revision		Revision as of 11:57, 11 December 2012
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	Association results can be uploaded to our web server using the [http://csg.sph.umich.edu/locuszoom/ plot your data webpage]. Result files are limited to 20Mb in size, which allows for a [[gzip\|gzipped]] text table including key columns (marker name, p-value and sample size) for up to ~3 million SNPs. In our tests, a typical GWAS results file is ~17 Mb in size after imputation of HapMap SNPs. Once a file is uploaded, LocusZoom will remember the file for the duration of your web session allowing you to generate multiple plots. If you have a slow connection or would like to save time, you can upload results for a region or chromosome of interest only. Your results are entirely confidential and won't be viewed by us or anyone else (except those with whom you share them!)		Association results can be uploaded to our web server using the [http://csg.sph.umich.edu/locuszoom/ plot your data webpage]. Result files are limited to 20Mb in size, which allows for a [[gzip\|gzipped]] text table including key columns (marker name, p-value and sample size) for up to ~3 million SNPs. In our tests, a typical GWAS results file is ~17 Mb in size after imputation of HapMap SNPs. Once a file is uploaded, LocusZoom will remember the file for the duration of your web session allowing you to generate multiple plots. If you have a slow connection or would like to save time, you can upload results for a region or chromosome of interest only. Your results are entirely confidential and won't be viewed by us or anyone else (except those with whom you share them!)

	To specify the region to be plotted, you will have to specify the name of a key marker in the region (typically, as an rs-number), name a gene of interest or provide appropriate genome coordinates. When displaying linkage disequilibrium, plotting will be very fast for small windows when HapMap CEU linkage disequilibrium is requested (because pairwise coefficients have been precomputed) and will be a bit slower for larger windows (because linkage disequilibrium coefficients must be computed on the fly).		To specify the region to be plotted, you will have to specify the name of a key marker in the region (typically, as an rs-number, but can be in chr:pos format), name a gene of interest or provide appropriate genome coordinates. When displaying linkage disequilibrium, plotting will be very fast for small windows when HapMap CEU linkage disequilibrium is requested (because pairwise coefficients have been precomputed) and will be a bit slower for larger windows (because linkage disequilibrium coefficients must be computed on the fly).

	If you include a sample size column in the result file, it will be used to control the size of each plotted marker.		If you include a sample size column in the result file, it will be used to control the size of each plotted marker.

Cristen: /* Commonly Used LocusZoom Options */

2010-09-10T09:39:30Z

Commonly Used LocusZoom Options

← Older revision		Revision as of 05:39, 10 September 2010
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	\| Reference Population for LD		\| Reference Population for LD
	\| n/a		\| n/a
	\| This option allows the user to specify which reference panel 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).		\| This option allows the user to specify which reference panel 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 or June 2010 release).
	\|-		\|-
	\| Highlight Region of Interest		\| Highlight Region of Interest

Cristen: /* Plotting of Pairwise Linkage Disequilibrium */

2010-06-10T19:59:46Z

Plotting of Pairwise Linkage Disequilibrium

← Older revision		Revision as of 15:59, 10 June 2010
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	=== Plotting of Pairwise Linkage Disequilibrium ===		=== Plotting of Pairwise Linkage Disequilibrium ===

	In the main plot window, data points are colored according to their level of linkage disequilibrium (LD) of the each SNP 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 genome coordinates or a gene name, LocusZoom will automatically select the most significant SNP in the region as the index SNP. For all other SNPs in the plot, the color of the data point will reflect the pairwise LD with this index SNP. The default LD measure is r<sup>2</sup> calculated from the HapMap CEU population (release 22), but users have the option to replace this with D’ and of selecting the HapMap YRI, Hapmap CHB+JPT or 1000 Genomes CEU reference panels. Because we have pre-computed LD for all SNPs in HapMap CEU, plots will often generate more quickly if using the default LD information. SNPs with missing LD information are shown in grey.		In the main plot window, data points are colored according to their level of linkage disequilibrium (LD) of the each SNP 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 genome coordinates or a gene name, LocusZoom will automatically select the most significant SNP in the region as the index SNP. For all other SNPs in the plot, the color of the data point will reflect the pairwise LD with this index SNP. The default LD measure is r<sup>2</sup> calculated from the HapMap CEU population (release 22), but users have the option to replace this with D’ and of selecting the HapMap YRI, Hapmap CHB+JPT or 1000 Genomes CEU reference panels. To display LD from 1000G CEU, please substitute rsid's for 1000G naming convention (chrxx:xxxx) whenever possible. Because we have pre-computed LD for all SNPs in HapMap CEU, plots will often generate more quickly if using the default LD information. SNPs with missing LD information are shown in grey.

	=== Customizing the Display of Your Results ===		=== Customizing the Display of Your Results ===

Cristen: /* Commonly Used LocusZoom Options */

2010-06-07T16:32:19Z

Commonly Used LocusZoom Options

← Older revision		Revision as of 12:32, 7 June 2010
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	\|}		\|}

	For a full list of options that can be used in Batch Mode using a hitspec file, please see [http://genome.sph.umich.edu/wiki/LocusZoom_Standalone#~~LocusZoom_options~~ this list]		For a full list of options that can be used in Batch Mode using a hitspec file, please see [http://genome.sph.umich.edu/wiki/LocusZoom_Standalone#Plotting_options this list]

	[[Category:Software]]		[[Category:Software]]

Cristen: /* Commonly Used LocusZoom Options */

2010-06-07T16:31:39Z

Commonly Used LocusZoom Options

← Older revision		Revision as of 12:31, 7 June 2010
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	\|}		\|}

			For a full list of options that can be used in Batch Mode using a hitspec file, please see [http://genome.sph.umich.edu/wiki/LocusZoom_Standalone#LocusZoom_options this list]

	[[Category:Software]]		[[Category:Software]]

Cristen at 15:12, 7 June 2010

2010-06-07T15:12:14Z

← Older revision		Revision as of 11:12, 7 June 2010
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	; 4. Download LocusZoom and run on your local unix machine		; 4. Download LocusZoom and run on your local unix machine
	: *[http://genome.sph.umich.edu/wiki/LocusZoom_Standalone Download LocusZoom] and [http://genome.sph.umich.edu/wiki/LocusZoom_Standalone#Sources_of_SQLite_database_tables associated databases]		: [http://genome.sph.umich.edu/wiki/LocusZoom_Standalone Download LocusZoom] and [http://genome.sph.umich.edu/wiki/LocusZoom_Standalone#Sources_of_SQLite_database_tables associated databases]

Cristen at 15:12, 7 June 2010

2010-06-07T15:12:03Z

← Older revision		Revision as of 11:12, 7 June 2010
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	; 4. Download LocusZoom and run on your local unix machine		; 4. Download LocusZoom and run on your local unix machine
	*[http://genome.sph.umich.edu/wiki/LocusZoom_Standalone Download LocusZoom] and [http://genome.sph.umich.edu/wiki/LocusZoom_Standalone#Sources_of_SQLite_database_tables associated databases]		: *[http://genome.sph.umich.edu/wiki/LocusZoom_Standalone Download LocusZoom] and [http://genome.sph.umich.edu/wiki/LocusZoom_Standalone#Sources_of_SQLite_database_tables associated databases]