Genezoom - Revision history

Ppwhite: /* Download from webpage */

2016-03-16T15:40:33Z

Download from webpage

← Older revision		Revision as of 11:40, 16 March 2016
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	== Get geneZoom Source Codes ==		== Get geneZoom Source Codes ==

	~~=== Download from webpage ===~~
	~~Through this link [http://www.sph.umich.edu/csg/jich/GeneZoom/ geneZoom Download], you can download a copy of geneZoom.~~

	=== Download from GitHub with Git ===		=== Download from GitHub with Git ===

Jchen: /* Get geneZoom Source Codes */

2014-10-23T13:26:36Z

Get geneZoom Source Codes

← Older revision		Revision as of 09:26, 23 October 2014
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	=== Download from webpage ===		=== Download from webpage ===
	Through this link [http://www.sph.umich.edu/csg/jich/~~geneZoom~~/ geneZoom Download], you can download a copy of geneZoom.		Through this link [http://www.sph.umich.edu/csg/jich/GeneZoom/ geneZoom Download], you can download a copy of geneZoom.

	=== Download from GitHub with Git ===		=== Download from GitHub with Git ===

Jchen at 09:45, 16 September 2014

2014-09-16T09:45:44Z

← Older revision		Revision as of 05:45, 16 September 2014
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	After you unzip, you can find 3 directories in "geneZoom" (./example ./lib ./scripts ./ref).		After you unzip, you can find 3 directories in "geneZoom" (./example ./lib ./scripts ./ref).


	== Basic Usage Example ==		== Basic Usage Example ==

Jchen: /* Parameters */

2014-09-16T09:25:16Z

Parameters

← Older revision		Revision as of 05:25, 16 September 2014
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	== Parameters ==		== Parameters ==
	'''vcf''': The VCF file has SNP information. This VCF must have header with sample ID.		'''vcf''': The VCF file has SNP information. This VCF must have header with sample ID. It can be a gz file or ASCII file.

	'''gene''': The gene region will be plotted. For example, "PCSK9".		'''gene''': The gene region will be plotted. For example, "PCSK9".

Jchen: /* Acknowledgements */

2014-09-16T08:37:09Z

Acknowledgements

← Older revision		Revision as of 04:37, 16 September 2014
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	== Acknowledgements ==		== Acknowledgements ==
	geneZoom is the result of collaborative efforts by Cristen Willer, Jin Chen, He zhang, Ellen Schmidt, Wei Zhou, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] with any questions.		'''geneZoom''' is the result of collaborative efforts by Cristen Willer, Jin Chen, He zhang, Ellen Schmidt, Wei Zhou, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] with any questions.

Jchen: /* Parameters */

2014-09-16T08:36:43Z

Parameters

Show changes

Jchen: /* Parameters */

2014-09-16T08:29:12Z

Parameters

← Older revision		Revision as of 04:29, 16 September 2014
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	'''vcf''': The VCF file has SNP information. This VCF must have header with sample ID.		'''vcf''': The VCF file has SNP information. This VCF must have header with sample ID.

	''gene'': The gene region will be plotted. For example, "PCSK9".		''''gene'''': The gene region will be plotted. For example, "PCSK9".

	phenotypeFile: The phenotype has phenotype value and sample ID. This file must have header to spcify which colum is phenotype value and sample ID.		phenotypeFile: The phenotype has phenotype value and sample ID. This file must have header to spcify which colum is phenotype value and sample ID.

Jchen: /* Parameters */

2014-09-16T08:28:57Z

Parameters

← Older revision		Revision as of 04:28, 16 September 2014
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	== Parameters ==		== Parameters ==
	vcf: The VCF file has SNP information. This VCF must have header with sample ID.		'''vcf''': The VCF file has SNP information. This VCF must have header with sample ID.

	gene: The gene region will be plotted. For example, "PCSK9".		''gene'': The gene region will be plotted. For example, "PCSK9".

	phenotypeFile: The phenotype has phenotype value and sample ID. This file must have header to spcify which colum is phenotype value and sample ID.		phenotypeFile: The phenotype has phenotype value and sample ID. This file must have header to spcify which colum is phenotype value and sample ID.
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	outDIR The result directory. All intermediate files and result plot		outDIR The result directory. All intermediate files and result plot
	file are in this folder.		file are in this folder.


	== Testing geneZoom ==		== Testing geneZoom ==

Jchen at 08:28, 16 September 2014

2014-09-16T08:28:37Z

← Older revision		Revision as of 04:28, 16 September 2014
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	You can get the help document.		You can get the help document.

			== Parameters ==
			vcf: The VCF file has SNP information. This VCF must have header with sample ID.

			gene: The gene region will be plotted. For example, "PCSK9".

			phenotypeFile: The phenotype has phenotype value and sample ID. This file must have header to spcify which colum is phenotype value and sample ID.

			sampleFieldName: The field name of sample ID in the phenotype file.

			phenotypeFieldName: The field name of phenotype value in the phenotype file

			phenotypeDelim: The delim in phenotype file. It can be tab, blank or comma.

			snpList: SNP list which you want to show in plot. If you have a lot SNPs
			in the gene region, you can specify the SNPs only shown in the
			plot. Can be NULL.

			snpChrFieldName
			The field name of CHR in SNP list. If you don't define snpList,
			this Can be NULL.

			snpPosFieldName
			The field name of POS in SNP list. If you don't define snpList,
			this Can be NULL.

			snpChrPosFieldName
			The field name of CHR:POS in SNP list. If you don't define
			snpList, this Can be NULL.

			snpDelim
			The delim in snp list. It can be tab, blank or comma. If you
			don't define snpList, this Can be NULL.

			lableSNPs
			The SNP which will be labled in plot. Can be NULL.

			flags The annotation values, MAF range and colors. For example,
			splicing:0:0.01:red,readthrough:blue. You must specify
			annotation value,MAF range and color can be empty. The tool will
			use the default MAF range(0,0.5), and random select one color.

			defaultIntron
			The default intron lenght in plot. When draw enxon region, tool
			re-define the intron region with this value. Can be NULL.

			title The titile of the plot. Can be NULL.

			xlab The xlab of the plot. Can be NULL.

			ylab The xlab of the plot. Can be NULL.

			titleCex
			The cex of title. This value can change the size of title. Can
			be NULL.

			xlabCex The cex of xlab. This value can change the size of xlab. Can be
			NULL.

			ylabCex The cex of ylab. This value can change the size of ylab. Can be
			NULL.

			scatterYAxisCex
			The cex of y axis. This value can change the size of y axis. Can
			be NULL.

			phenotyeMeanLineColor
			The color of mean value of all SNPs in gene region. Can be NULL.

			phenotyeMeanLineType
			The line type of mean value of all SNPs in gene region. Can be
			NULL.

			phenotyeSDLineColor
			The color of standard deviation value of all SNPs in gene
			region. Can be NULL.

			phenotyeSDLineType
			The line type of standard deviation value of all SNPs in gene
			region. Can be NULL.

			exonRegionColor
			The color of exon region. Can be NULL.

			beanPlotXAxisLabelAngle
			The lable angle of bean plot x axis. Can be NULL.

			beanPlotXAxisLableCex
			The cex of bean plot x axis. Can be NULL.

			beanPlotXAxisLablePos1
			The position 1 of bean plot x axis lable. Can be NULL.

			beanPlotXAxisLablePos2
			The position 2 of bean plot x axis lable. Can be NULL.

			width The width of plot. Default is 14.1 . Can be NULL.

			height The height of plot. Default is 10. Can be NULL.

			format The format of plot. It can be pdf,tiff and png. Can be NULL.

			outDIR The result directory. All intermediate files and result plot
			file are in this folder.


			== Testing geneZoom ==
			There is an example directory in ~/geneZoom. You can find vcf file, phenotype file and on sh file.
			Run geneZoom example.sh.

			sh ~/geneZoom/example/example.sh

			After running 2 minutes +/- 1 minutes. You will get result file "PCSK9.pdf" in your defined output directory.

			== Acknowledgements ==
			geneZoom is the result of collaborative efforts by Cristen Willer, Jin Chen, He zhang, Ellen Schmidt, Wei Zhou, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] with any questions.

Jchen: /* Basic Usage Example */

2014-09-16T02:42:57Z

Basic Usage Example

← Older revision		Revision as of 22:42, 15 September 2014
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	perl GeneZoom.pl --vcf vcf --phenotypeFile phenotypeFile --sampleFieldName sample --phenotypeFieldName phenotype --phenotypeDelim tab/comma/blank --snpList snpList --snpChrFieldName chr --snpPosFieldName pos --snpDelim tab/comma/blank --flag "splicing:green,nonsense:0.02:0.03,missense" --lables "chr1:123,chr2:234" --outDIR outDIR		perl GeneZoom.pl --vcf vcf --phenotypeFile phenotypeFile --sampleFieldName sample --phenotypeFieldName phenotype --phenotypeDelim tab/comma/blank --snpList snpList --snpChrFieldName chr --snpPosFieldName pos --snpDelim tab/comma/blank --flag "splicing:green,nonsense:0.02:0.03,missense" --lables "chr1:123,chr2:234" --outDIR outDIR
	--------------------------------------		--------------------------------------

			== Get Help ==
			When you run
			perl geneZoom.pl --man
			perl geneZoom.pl --help
			perldoc geneZoom.pl

			You can get the help document.