Recently, I analyzed genomic features including CNV, indel and SNV across around 50 cell lines.
I would like to know the significant factors to give cancerous properties to those cell lines.
So, I want to retrieve number of cases from TCGA data.
My hypothesis is that if count 0, it is a kind of not significant.
I know that someone already post a similar question.(Retreiving Data From Tcga Database)
However, as I have thousands of rows of mutation spots, I really hope to find a program to annotate the number of TCGA cases.
The coordinates columns are below.
2. Location (numeric)
3. Reference base information
4. Altered base information
5. Genes(Gene symbols)
Please, suggest any program or method to make column for TCGA number cases.