Hi ,

In the documentation "cnTable Custom copynumber data if gistic results are not available. Input file should a tab seperated three column table containing gene name, Sample name and copy number status".

How should i create a cnTable if there is Amplification/Deletion for a particular gene in multiple sample?

Hi,

Apologies for late reply. Did you figure it out ? cnTable should be a tsv file with above mentioned columns. Something like this:

genes   tsb     cn
TTN     TCGA.AB.2814    Amp
NRAS    TCGA.AB.2872    Del
TP53    TCGA.AB.2957    Amp
NPM1    TCGA.AB.2904    Del
SMC3    TCGA.AB.2824    Amp
SMC1A   TCGA.AB.2898    Amp
TTN     TCGA.AB.2917    Amp
TP53    TCGA.AB.2967    Del

Let me know if you have any questions.