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How to convert a CNV data into a matrix of row samples and column genes

Hello guys,

want to convert my cancer data which I got from the Broad Firehose (http://gdac.broadinstitute.org) into a matrix (where the rows will represent the samples and the columns represent the genes).

However, in this data, there are many samples and each sample has many chromosomes(1-23) and many segments mean values

So, which samples have to take among the 23 chromosomes and which segment value?

CNV_data

I appreciate any help!

cnv processing
• 1,970 views • link
updated by finswimmer finswimmer • written by Chaimaa Chaimaa

Please do not add tabular text as a screenshot. You can:

  • add a HTML table; or
  • save it as a tab-separated file on your computer, then run cat tab_sep_file | column -ts $'\t' and copy-paste the output to a code-formatted block here; or
  • save it as a tab-separated file (ideally after running it through the column command as shown above for proper formatting), upload it to gist and add a link to the gist here
• 1 views • link
written by Ram Ram

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