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

Question

[Chaimaa]

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?

I appreciate any help!

[Ram]

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