CNA Processing

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)

Usage

Rscript R/CNA_processing.R -h                                       
usage: R/CNA_processing.R [-h] [-m MASTERREF] [-o RESULTSDIR] [-dmp DMPDIR]

optional arguments:
  -h, --help            show this help message and exit
  -m MASTERREF, --masterref MASTERREF
                        File path to master reference file
  -o RESULTSDIR, --resultsdir RESULTSDIR
                        Output directory
  -dmp DMPDIR, --dmpdir DMPDIR
                        Directory of clinical DMP IMPACT repository [default]

What CNA_processing.R does

1. Process DMP CNAs

2. Process ACCESS CNAs

3. CNA 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