analyze_yours_manhattan

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analyze_yours_manhattan [2019/07/06 13:08]
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analyze_yours_manhattan [2019/07/06 13:09] (current)
tongyifan
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 ====== Analyze yours: Manhattan plot ====== ====== Analyze yours: Manhattan plot ======
  
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 //Note: quick help can be available through putting your mouse on the small question marks besides certain options in this pages.// //Note: quick help can be available through putting your mouse on the small question marks besides certain options in this pages.//
  
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-{{  http://​www.clickgenome.org/​img/​guide/​1001.png ​ }}+{{  http://​www.clickgenome.org/​img/​guide/​1001.png?​direct& ​ }}
  
 ===== Setting area ===== ===== Setting area =====
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 4. You can specify concern gene here by inputting gene symbols. Only symbols provided in your files are accepted. If you want to input more than one gene symbols, a common and a space should be used to separate two gene symbols. 4. You can specify concern gene here by inputting gene symbols. Only symbols provided in your files are accepted. If you want to input more than one gene symbols, a common and a space should be used to separate two gene symbols.
  
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 //Note: small case and big case are all acceptable. For example, kRAS, kras, KRas, KRAS are all treated as the same gene.// //Note: small case and big case are all acceptable. For example, kRAS, kras, KRas, KRAS are all treated as the same gene.//
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 The 'Save as Image' button will show up at the top right of this plotting area when a Manhattan plot is created. You can click it to swich into a image saving webpage then click right mouse button to save this image. You also can specify the image format and size by selecting the options in the Figure downloading and DIY area. The 'Save as Image' button will show up at the top right of this plotting area when a Manhattan plot is created. You can click it to swich into a image saving webpage then click right mouse button to save this image. You also can specify the image format and size by selecting the options in the Figure downloading and DIY area.
  
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 For your convinence, the sample ID and other details of each individual gene will show up when you put your mouse on the corresponding line. For your convinence, the sample ID and other details of each individual gene will show up when you put your mouse on the corresponding line.
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 For example: in the above figure, after putting the mouse on a line, a catalog showed up like this: For example: in the above figure, after putting the mouse on a line, a catalog showed up like this:
  
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 From the left to the right are: gene symbol and p-value of this gene in the corresponding two groups. Therefore, in this example: the gene symbol is AIM1L, the p-value of it's copy number variations in the two group samples uploaded by the user is 4.18e-15 which means it has significantly different copy number variations in these two groups. From the left to the right are: gene symbol and p-value of this gene in the corresponding two groups. Therefore, in this example: the gene symbol is AIM1L, the p-value of it's copy number variations in the two group samples uploaded by the user is 4.18e-15 which means it has significantly different copy number variations in these two groups.
  
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 ===== Figure downloading and DIY area ===== ===== Figure downloading and DIY area =====
  
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 ==== 1.Figure Downloading area: ==== ==== 1.Figure Downloading area: ====
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 → Please put gene symbols of each group in the first column. If you don't have them, please use numbers or something as symbols. In Mountain plot, the corresponding gene symbol will show up when you put your mouse on any markers. If there are more than one groups, only genes that are common in all groups will be plotted. Therefore, they are necessary information for creating the plot. → Please put gene symbols of each group in the first column. If you don't have them, please use numbers or something as symbols. In Mountain plot, the corresponding gene symbol will show up when you put your mouse on any markers. If there are more than one groups, only genes that are common in all groups will be plotted. Therefore, they are necessary information for creating the plot.
  
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 → Please put the start location for the genes in the second column. They will be used as the x-axis values in the Mountain plot. → Please put the start location for the genes in the second column. They will be used as the x-axis values in the Mountain plot.
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 Since the Directional Manhattan box is checked, the positive y-axis values of them means the mean values of the copy numbers of genes in group are all bigger than what in group2. Since the Directional Manhattan box is checked, the positive y-axis values of them means the mean values of the copy numbers of genes in group are all bigger than what in group2.
  
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  • analyze_yours_manhattan.txt
  • Last modified: 2019/07/06 13:09
  • by tongyifan