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:

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