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Genezoom (view source)

Revision as of 11:40, 16 March 2016

427 bytes removed ,  11:40, 16 March 2016
→‎Download from webpage
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== Get geneZoom Source Codes ==
 
== Get geneZoom Source Codes ==
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=== Download from webpage ===
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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 ===
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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).
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== Basic Usage Example ==
 
== Basic Usage Example ==
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== Parameters ==
 
== Parameters ==
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vcf: The VCF file has SNP information. This VCF must have header with sample ID.
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'''vcf''': The VCF file has SNP information. This VCF must have header with sample ID. It can be a gz file or ASCII file.
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gene: The gene region will be plotted. For example, "PCSK9".
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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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'''gene''': The gene region will be plotted. For example, "PCSK9".
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sampleFieldName: The field name of sample ID in the phenotype file.
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'''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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phenotypeFieldName: The field name of phenotype value in the phenotype file
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'''sampleFieldName''': The field name of sample ID in the phenotype file.
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phenotypeDelim: The delim in phenotype file. It can be tab, blank or comma.
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'''phenotypeFieldName''': The field name of phenotype value in the phenotype file
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snpList: SNP list which you want to show in plot. If you have a lot SNPs
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'''phenotypeDelim''': The delim in phenotype file. It can be tab, blank or comma.
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            in the gene region, you can specify the SNPs only shown in the
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            plot. Can be NULL.
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    snpChrFieldName
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'''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.
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            The field name of CHR in SNP list. If you don't define snpList,
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            this Can be NULL.
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    snpPosFieldName
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'''snpChrFieldName''': The field name of CHR in SNP list. If you don't define snpList, this Can be NULL.
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            The field name of POS in SNP list. If you don't define snpList,
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            this Can be NULL.
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    snpChrPosFieldName
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'''snpPosFieldName''': The field name of POS in SNP list. If you don't define snpList, this Can be NULL.
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            The field name of CHR:POS in SNP list. If you don't define
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            snpList, this Can be NULL.
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    snpDelim
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'''snpChrPosFieldName''': The field name of CHR:POS in SNP list. If you don't define snpList, this Can be NULL.
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            The delim in snp list. It can be tab, blank or comma. If you
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            don't define snpList, this Can be NULL.
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    lableSNPs
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'''snpDelim''': The delim in snp list. It can be tab, blank or comma. If you don't define snpList, this Can be NULL.
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            The SNP which will be labled in plot. Can be NULL.
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    flags  The annotation values, MAF range and colors. For example,
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'''lableSNPs''': The SNP which will be labled in plot. Can be NULL.
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            splicing:0:0.01:red,readthrough:blue. You must specify
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            annotation value,MAF range and color can be empty. The tool will
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            use the default MAF range(0,0.5), and random select one color.
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    defaultIntron
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'''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.
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            The default intron lenght in plot. When draw enxon region, tool
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            re-define the intron region with this value. Can be NULL.
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    title  The titile of the plot. Can be NULL.
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'''defaultIntron''': The default intron lenght in plot. When draw enxon region, tool re-define the intron region with this value. Can be NULL.
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    xlab    The xlab of the plot. Can be NULL.
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'''title''': The titile of the plot. Can be NULL.
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    ylab    The xlab of the plot. Can be NULL.
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'''xlab''': The xlab of the plot. Can be NULL.
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    titleCex
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'''ylab''': The xlab of the plot. Can be NULL.
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            The cex of title. This value can change the size of title. Can
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            be NULL.
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    xlabCex The cex of xlab. This value can change the size of xlab. Can be
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'''titleCex''': The cex of title. This value can change the size of title. Can be NULL.
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            NULL.
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    ylabCex The cex of ylab. This value can change the size of ylab. Can be
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'''xlabCex''': The cex of xlab. This value can change the size of xlab. Can be NULL.
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            NULL.
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    scatterYAxisCex
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'''ylabCex''': The cex of ylab. This value can change the size of ylab. Can be NULL.
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            The cex of y axis. This value can change the size of y axis. Can
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            be NULL.
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    phenotyeMeanLineColor
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'''scatterYAxisCex''': The cex of y axis. This value can change the size of y axis. Can be NULL.
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            The color of mean value of all SNPs in gene region. Can be NULL.
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    phenotyeMeanLineType
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'''phenotyeMeanLineColor''': The color of mean value of all SNPs in gene region. Can be NULL.
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            The line type of mean value of all SNPs in gene region. Can be
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            NULL.
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    phenotyeSDLineColor
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'''phenotyeMeanLineType''': The line type of mean value of all SNPs in gene region. Can be NULL.
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            The color of standard deviation value of all SNPs in gene
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            region. Can be NULL.
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    phenotyeSDLineType
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'''phenotyeSDLineColor''': The color of standard deviation value of all SNPs in gene region. Can be NULL.
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            The line type of standard deviation value of all SNPs in gene
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            region. Can be NULL.
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    exonRegionColor
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'''phenotyeSDLineType''': The line type of standard deviation value of all SNPs in gene region. Can be NULL.
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            The color of exon region. Can be NULL.
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    beanPlotXAxisLabelAngle
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'''exonRegionColor''': The color of exon region. Can be NULL.
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            The lable angle of bean plot x axis. Can be NULL.
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    beanPlotXAxisLableCex
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'''beanPlotXAxisLabelAngle''': The lable angle of bean plot x axis. Can be NULL.
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            The cex of bean plot x axis. Can be NULL.
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    beanPlotXAxisLablePos1
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'''beanPlotXAxisLableCex''': The cex of bean plot x axis. Can be NULL.
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            The position 1 of bean plot x axis lable. Can be NULL.
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    beanPlotXAxisLablePos2
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'''beanPlotXAxisLablePos1''': The position 1 of bean plot x axis lable. Can be NULL.
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            The position 2 of bean plot x axis lable. Can be NULL.
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    width  The width of plot. Default is 14.1 . Can be NULL.
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'''beanPlotXAxisLablePos2''': The position 2 of bean plot x axis lable. Can be NULL.
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    height  The height of plot. Default is 10. Can be NULL.
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'''width''': The width of plot. Default is 14.1 . Can be NULL.
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    format  The format of plot. It can be pdf,tiff and png. Can be NULL.
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'''height''': The height of plot. Default is 10. Can be NULL.
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    outDIR  The result directory. All intermediate files and result plot
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'''format''': The format of plot. It can be pdf,tiff and png. Can be NULL.
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            file are in this folder.
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'''outDIR''': The result directory. All intermediate files and result plot file are in this folder.
    
== Testing geneZoom ==
 
== Testing geneZoom ==
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== Acknowledgements  ==
 
== Acknowledgements  ==
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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.
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'''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.
Ppwhite
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11593...14135"

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