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bioinf-jku / panelcn.mops

CNV detection tool for targeted NGS panel data
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how to extract the cn values to plot #17

Open QuanLG opened 4 years ago

QuanLG commented 4 years ago

Hello, I want to plot a copy number variation picture, I try to extract the values like this:

微信图片_20191220134638

    I found all the region is the same value close to 1  ,so I want to know which value and how to extract that I can plot a picture like this:

cnv_20191220135036

gpovysil commented 4 years ago

Sorry for the late reply. The plots you show are not part of panelcn.mops and I'm not sure what you are looking for. The values in the cn.mops object you highlighted are posterior probabilities not RC ratios. You could calculate a ratio by using columns of the resulttable (created with panelcn.mops function createResultTable): ratio = RC.norm/medRC.norm

QuanLG commented 4 years ago

the plot use the result of cns and cnr which are both output from cnvkit to show the copy number,so I want have a plot like this . I try to use the result of panelcnv to estimate the longer segment by R package DNAcopy,I noticed that the DNAcopy use the logratio (aCGH, ROMA, etc.) or binary (LOH) and CBS to estimate the longer segment,so I want to extract the ration from the panelcnv . Recently,I use 'logRatios <- cn.mops:::.makeLogRatios(res)' to extract the ration,but I find some logrations are greater than 1.5 ,but the CN type is CN0. so if I can use the logrations to estimate the longer segment?