Update value formats in the MTP CNV frequencies table

[ewafula]

Purpose/implementation Section

What scientific question is your analysis addressing?

update cnv-frequencies module values format

What was your approach?

the cnv frequencies module output table for Total_relapse_tumors_mutated_over_primary_tumors_in_dataset and Total_relapse_tumors_mutated_over_relapse_tumors_in_dataset columns to include a denominator value where there are no samples for a particular CNV Variant_type.

What GitHub issue does your pull request address?

• Investigate value formats in the MTP CNV frequencies table  ticket-tracker-OPC#467

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Check for cancer groups that had zero as a denominator for the Total_relapse_tumors_mutated_over_primary_tumors_in_dataset and Total_relapse_tumors_mutated_over_relapse_tumors_in_dataset columns some but not all CNV Variant_type now have the required denominator value representing either the number of primary or relapse samples in the cancer group.

Examples should as following as opposed to what is illustrated in the issue ticket:

> read_tsv("../cnv-frequencies/results/gene-level-cnv-consensus-annotated-mut-freq.tsv.gz") %>% filter(Gene_symbol == "CFTR", Disease == "Diffuse midline glioma") %>% select(Variant_type, Dataset, Disease, Total_relapse_tumors_mutated_over_relapse_tumors_in_dataset, Frequency_in_relapse_tumors)

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
# A tibble: 4 x 5
  Variant_type  Dataset Disease                Total_relapse_tumors_mu~1 Frequ~2
  <chr>         <chr>   <chr>                  <chr>                     <chr>  
1 amplification PBTA    Diffuse midline glioma 0/7                       0.00%  
2 gain          PBTA    Diffuse midline glioma 0/7                       0.00%  
3 loss          PBTA    Diffuse midline glioma 1/7                       14.29% 
4 neutral       PBTA    Diffuse midline glioma 0/7                       0.00%  
# ... with abbreviated variable names
#   1: Total_relapse_tumors_mutated_over_relapse_tumors_in_dataset,
#   2: Frequency_in_relapse_tumors
> 

Is there anything that you want to discuss further?

NA

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

YES

Results

What types of results are included (e.g., table, figure)?

Tables

What is your summary of the results?

• gene-level-cnv-consensus-annotated-mut-freq.jsonl.gz
• gene-level-cnv-consensus-annotated-mut-freq.tsv.gz

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[sangeetashukla]

@ewafula I reviewed the logic in the script including the correct denominator value for CNV variant_type, ran the script and reviewed the result files. It looks correct now.