> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/cmo-access-data-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/cmo-access-data-analysis/analysis/cna-processing.md).

# 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](https://github.com/msk-access/access_data_analysis/blob/17a26eea455707c82824493ebc597d9850d47e82/R/CNA_processing.R#L19-L25)&#x20;
2. [Process ACCESS CNAs](https://github.com/msk-access/access_data_analysis/blob/17a26eea455707c82824493ebc597d9850d47e82/R/CNA_processing.R#L29-L33)&#x20;
3. [CNA Calling](https://github.com/msk-access/access_data_analysis/blob/17a26eea455707c82824493ebc597d9850d47e82/R/CNA_processing.R#L36-L44) (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 |
| ---------------------- | ---------------- | ------------ | ----- | -- | ---------- | --- | ---------------- |
|                        |                  |              |       |    |            |     |                  |