LocusZoom Standalone - Revision history

Abought at 22:03, 18 November 2021

2021-11-18T22:03:24Z

← Older revision		Revision as of 18:03, 18 November 2021
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	<br> [[Image:LocusZoomSmall.png]]		<br> [[Image:LocusZoomSmall.png]]

	This page contains information regarding a version of LocusZoom that may be downloaded for personal use. For more information on LocusZoom, see this [[LocusZoom\|page]].		This page contains information regarding a version of LocusZoom that may be downloaded for personal use. For more information on LocusZoom, see this [[LocusZoom\|page]]. '''This page refers to the command line "standalone" version, which is no longer actively maintained. For information about a web-friendly version with support for modern datasets, see [https://github.com/statgen/locuszoom LocusZoom.js] on GitHub, or [https://my.locuszoom.org https://my.locuszoom.org] to plot your own data''' .

	To be notified of future changes to LocusZoom, you can join our [http://groups.google.com/group/locuszoom Google Group].		To be notified of future changes to LocusZoom, you can join our [http://groups.google.com/group/locuszoom Google Group].

2018-05-16T17:00:39Z

METAL formatted file

← Older revision		Revision as of 13:00, 16 May 2018
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	\| align="center" \| 1.23e-04		\| align="center" \| 1.23e-04
	\|-		\|-
	\| align="center" \| ~~rs3~~		\| align="center" \| chr4:401141
	\| align="center" \| 9.4e-390		\| align="center" \| 9.4e-390
	\|}		\|}

	<br>		<br>

			Markers can be either rsIDs or chr:pos format (see above).

	This file should be passed to locuszoom using the <code>--metal</code> option.		This file should be passed to locuszoom using the <code>--metal</code> option.

2017-05-31T18:28:16Z

@@ Line 29: / Line 29: @@
-For the latest stable LocusZoom package, see our [https://statgen.sph.umich.edu/locuszoom/download/ download] page. The current version is '''1.3''', released on June 20th, 2014.
+For the latest stable LocusZoom package, see our [https://github.com/statgen/locuszoom-standalone download] page. The current version is '''1.3''', released on June 20th, 2014.
 Currently only '''Unix/Linux''' is supported, though Mac OS X should be supported in a future release. Support for Windows may come at a much later date.
@@ Line 45: / Line 45: @@
 == Download ==
-See our [https://statgen.sph.umich.edu/locuszoom/download/ download] page for links to the latest as well as previous releases.
+See our [https://github.com/statgen/locuszoom-standalone download] page for links to the latest as well as previous releases.
 == Installation  ==

2016-05-02T21:04:05Z

Plotting BED tracks

← Older revision		Revision as of 17:04, 2 May 2016
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	</pre>		</pre>

	The BED file should have at least 4 columns: the first 3 for chr/start/end, and the 4th column for the label of the track.		The BED file should have at least 4 columns: the first 3 for chr/start/end, and the 4th column for the label of the track. It must be '''tab-delimited''', not white-space delimited.

	Color can also be specified, but the BED file then needs to follow the full [http://genome.ucsc.edu/FAQ/FAQformat.html#format1 BED format].		Color can also be specified, but the BED file then needs to follow the full [http://genome.ucsc.edu/FAQ/FAQformat.html#format1 BED format].

2015-01-13T01:50:53Z

Plotting options

← Older revision		Revision as of 21:50, 12 January 2015
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	\|-		\|-
	\| colorCol=NULL		\| colorCol=NULL
	\| Specify the name of a column in association results file denoting the color each marker should be. This disables coloring by LD. ~~Color~~ names should be used, for example "red" "olivedrab" etc.		\| Specify the name of a column in association results file denoting the color each marker should be. This disables coloring by LD. For the column values, color names should be used, for example "red" "olivedrab" etc.
	\|-		\|-
	\| signifLine=NULL		\| signifLine=NULL

2015-01-13T01:50:32Z

Plotting options

← Older revision		Revision as of 21:50, 12 January 2015
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	\|-		\|-
	\| colorCol=NULL		\| colorCol=NULL
	\| Specify the name of a column in association results file denoting the color each marker should be. This disables coloring by LD.		\| Specify the name of a column in association results file denoting the color each marker should be. This disables coloring by LD. Color names should be used, for example "red" "olivedrab" etc.
	\|-		\|-
	\| signifLine=NULL		\| signifLine=NULL

2015-01-13T01:50:02Z

← Older revision		Revision as of 21:50, 12 January 2015
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	\|-		\|-
	\| signifLine=NULL		\| signifLine=NULL
	\| Specify (in p-value scale) where to place a horizontal significance line. Can have multiple lines, e.g. signifLine="~~5e-08~~,~~1e-10~~"		\| Specify (in -log10 p-value scale) where to place a horizontal significance line. Can have multiple lines, e.g. signifLine="7.3,9"
	\|-		\|-
	\| signifLineColor=NULL		\| signifLineColor=NULL

2014-09-03T04:14:44Z

Plotting BED tracks

← Older revision		Revision as of 00:14, 3 September 2014
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	</pre>		</pre>

	The BED file should have 4 columns: the first 3 for chr/start/end, and the 4th column for the label of the track.		The BED file should have at least 4 columns: the first 3 for chr/start/end, and the 4th column for the label of the track.

			Color can also be specified, but the BED file then needs to follow the full [http://genome.ucsc.edu/FAQ/FAQformat.html#format1 BED format].

	=== Specify gene table (refFlat, GENCODE, etc.) ===		=== Specify gene table (refFlat, GENCODE, etc.) ===

2014-09-01T17:16:12Z

Fine-mapping credible sets

← Older revision		Revision as of 13:16, 1 September 2014
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	=== Fine-mapping credible sets ===		=== Fine-mapping credible sets ===

	LocusZoom can add an additional track to the plot showing results from a fine-mapping analysis. These are typically SNPs within the 95% credible set (see [http://www.nature.com/ng/journal/v44/n12/full/ng.2435.html this paper] for an example.)		LocusZoom can add an additional track to the plot showing results from a fine-mapping analysis. These are typically SNPs within the 95% credible set (see [http://www.nature.com/ng/journal/v44/n12/full/ng.2435.html this paper] for an example of a method generating such a set of SNPs.)

	To add this fine-mapping track, you supply (as a plotting option) the fine-mapping set of credible SNPs as a file:		To add this fine-mapping track, you supply (as a plotting option) the fine-mapping set of credible SNPs as a file:
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	[[File:New lz finemap summary.png\|400px]]		[[File:New lz finemap summary.png\|400px]]


	=== Labeling multiple SNPs ===		=== Labeling multiple SNPs ===

2014-06-27T00:41:03Z

Plotting BED tracks

← Older revision		Revision as of 20:41, 26 June 2014
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	<pre>		<pre>
	locuszoom ... --bed-~~file~~ <your file>		locuszoom ... --bed-tracks <your bed file>
	</pre>		</pre>