Fixed path in qc script, removed unwanted symbols from ensg mapping file

[sangeetashukla]

Purpose/implementation Section

Updated gene_match module to reflect correct path for the data files, and fix the ensg-hugo-pmtl-mapping.tsv file to filter out ensg_id = Symbol_Not_Found and gene_symbol = NA

What was your approach?

• Remove version (v10) specification from the qc_ensg_hugo_pmtl_mapping.Rmd script for reading in data files
• Add a filter to remove unwanted ensg_id and gene_symbol before writing to ensg-hugo-pmtl-mapping.tsv in the add_pmtl_ens_hugo.Rmd script

What GitHub issue does your pull request address?

Issue 231

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

Please test if the scripts run as expected with symlink set up to read data files.

Is there anything that you want to discuss further?

No

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)?

ensg-hugo-pmtl-mapping.tsv

What is your summary of the results?

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.

[ewafula]

@sangeetashukla, please change to the OpenPedCan-analysis/data directory to be relative to the qc_ensg_hugo_pmtl_mapping.Rmd location as I have shown in the code comment. Not everyone running the module will have the OpenPedCan-analysis local cloned repo in their home directory (~/). Otherwise, the results are ok. The Symbol_Not_Found and NA values in gene_symbol and ensg_id column respectively have been filtered out of the results/ensg-hugo-pmtl-mapping.tsv file.

Quitting from lines 17-46 (qc_ensg_hugo_pmtl_mapping.Rmd)
Error: ‘~/OpenPedCan-analysis/data//snv-consensus-plus-hotspots.maf.tsv.gz’ does not exist.

Execution halted

[ewafula]

Change to:
open_ped_can_data_path <- '../../data'

[sangeetashukla]

@sangeetashukla, please change to the OpenPedCan-analysis/data directory to be relative to the qc_ensg_hugo_pmtl_mapping.Rmd location as I have shown in the code comment. Not everyone running the module will have the OpenPedCan-analysis local cloned repo in their home directory (~/). Otherwise, the results are ok. The Symbol_Not_Found and NA values in gene_symbol and ensg_id column respectively have been filtered out of the results/ensg-hugo-pmtl-mapping.tsv file.

Quitting from lines 17-46 (qc_ensg_hugo_pmtl_mapping.Rmd)
Error: ‘~/OpenPedCan-analysis/data//snv-consensus-plus-hotspots.maf.tsv.gz’ does not exist.

Execution halted

Thank you @ewafula for catching that. I have updated the file path appropriately and tested the script.

[ewafula]

@sangeetashukla, trailing backslash is unnecessary. R will add when joining to create a path. Will still work but you will have double backslashes as shown in the previous error message that I posted.
set to this: open_ped_can_data_path <- '../../data'

[runjin326]

Thanks @sangeetashukla for preparing this! Everything looks good to me now (thanks @ewafula for the detailed review).
@sangeetashukla, could you please do a dev merge and I think this should be ready for merge.

[sangeetashukla]

Thanks @sangeetashukla for preparing this! Everything looks good to me now (thanks @ewafula for the detailed review). @sangeetashukla, could you please do a dev merge and I think this should be ready for merge.

@runjin326 Done