I am wanna to make a matrix [sample x genes] from CNV files, level 3, downloaded from TCGA database, but I don't know how can I do that.
Currently I have mapped the segments to genes with help of guys, so I have many genes for each segment. It should be noted that some of segments have common genes and it have made me confused.
I appreciate if anyone can help and introduce texts.
EDIT: To be more clear, I have downloaded CNV (SNP array) for BRCA from TCGA. Its link is here.