Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update vignette #212

Merged
merged 1 commit into from
Feb 13, 2025
Merged

Update vignette #212

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 6 additions & 5 deletions vignettes/bringing-portal-data-to-other-platforms-cbioportal.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ Each study dataset combines multiple data types -- clinical, gene expression, ge

cbp_new_study(cancer_study_identifier = "npst_nfosi_ntap_2022",
name = "Plexiform Neurofibroma and Neurofibroma (Pratilas 2022)",
type_of_cancer = "nfib", # required -- see https://oncotree.mskcc.org/
citation = "TBD")
```

Expand All @@ -77,7 +78,7 @@ Note that:

maf_data <- "syn36553188"

add_cbp_maf(maf_data)
cbp_add_maf(maf_data)
```

### Add copy number alterations (CNA) data
Expand Down Expand Up @@ -108,14 +109,14 @@ cbp_add_expression(mrna_data,

### Add clinical data

- `clinical_data` is a prepared clinical data table already subsetted to those released in this study, or pass in a query that can be used for subsetting if using a full clinical database table. For example, the full clinical cohort comprises patients 1-50, but this study dataset consists of available and releasable data only for patients 1-20 for expression data and data patients 15-20 for cna data. Here, `clinical_data` can be a smaller table of just those 1-30, or it can be the original table but pass in a suitable additional filter, e.g. `where release = 'batch1'`.
- Clinical data **should be added last**, after all other data has been added, for sample checks to work properly.
- `clinical_data` is prepared from an existing Synapse table. The table can be a subsetted version of those released in the study dataset, or pass in a query that can be used for getting the subset. For example, the full clinical cohort comprises patients 1-50, but the dataset can only release data for patients 1-20 for expression data and data patients 15-20 for cna data. Here, `clinical_data` can be a smaller table of just those 1-30, or it can be the original table but pass in a suitable additional filter, e.g. `where release = 'batch1'`.
- Clinical data requires mapping to be as consistent with other public datasets as possible. `ref_map` defines the mapping of clinical variables from the NF-OSI data dictionary to cBioPortal's. Only variables in the mapping are exported to cBioPortal. Follow link below to inspect the default file and format used.
- Clinical data should be added last for overall sample checks to work. For example, if there is expression data for patients 1-20 and cna data patients 15-20,
it can more informatively warn about any missing/mismatches.
- Clinical data **should be added last**, after all other data has been added, for sample checks to work properly.

```{r add_clinical, eval=FALSE}

clinical_data <- "select * from syn43278088"
clinical_data <- "select * from syn43278088" # query when the table already contains just the releasable patients
ref_map <- "https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/main/mappings/cBioPortal.yaml"

cbp_add_clinical(clinical_data, ref_map)
Expand Down
Loading