Step 4 -- generating final CNA call set
This step generates a final CNA call set for plotting. This consists of:
Calls passing de novo CNA calling threshold
Significant adjusted p value ( <= 0.05)
Significant fold change ( > 1.5 or < -1.5)
Calls that can be rescued based on prior knowledge from IMPACT samples
Significant adjusted p value ( <= 0.05)
Lowered threshold for fold change ( < 1.2 or < -1.2)
CNA_processing.R doesCNA Calling (de novo and rescue)
Format of the final call set:
Tumor_Sample_Barcode
cmo_patient_id
Hugo_Symbol
p.adj
fc
CNA_tumor
CNA
dmp_patient_id