docs/analysis/cna-processing.md

In msk-access/access_data_analysis: ACCESS data analysis

description: Step 4 -- generating final CNA call set

CNA Processing

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 | | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | | | | | | | | | |

msk-access/access_data_analysis documentation built on Nov. 13, 2023, 12:43 p.m.