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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.
