cbp_add_clinical: Export and add clinical data to cBioPortal dataset
In nf-osi/nfportalutils: NF Portal Utilities
cbp_add_clinical R Documentation
Export and add clinical data to cBioPortal dataset
Description
This should be run in an existing dataset package root.
Usage
cbp_add_clinical(clinical_data, ref_map, verbose = TRUE)
Arguments
clinical_data
Clinical table query.
ref_map
YAML file specifying the mapping of (NF) clinical metadata to cBioPortal model. See details.
verbose
Whether to provide informative messages throughout.
Details
Clinical data are mapped and exported according to a reference mapping.
Also reformatting of PATIENT_ID, SAMPLE_ID to contain only letters, numbers, points, underscores, hyphens;
in Nextflow processing any spaces gets replaced with underscores so that's the default here.
Does not check for missing samples, as final validation via cBioPortal tool is still expected for that.
nf-osi/nfportalutils documentation built on Feb. 26, 2024, 1:05 p.m.
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| cbp_add_clinical | R Documentation |
Export and add clinical data to cBioPortal dataset
Description
This should be run in an existing dataset package root.
Usage
cbp_add_clinical(clinical_data, ref_map, verbose = TRUE)
Arguments
clinical_data |
Clinical table query. |
ref_map |
YAML file specifying the mapping of (NF) clinical metadata to cBioPortal model. See details. |
verbose |
Whether to provide informative messages throughout. |
Details
Clinical data are mapped and exported according to a reference mapping.
Also reformatting of PATIENT_ID, SAMPLE_ID to contain only letters, numbers, points, underscores, hyphens;
in Nextflow processing any spaces gets replaced with underscores so that's the default here.
Does not check for missing samples, as final validation via cBioPortal tool is still expected for that.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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