Initialize a new cBioPortal study dataset — cbp_new

Create a new directory with a basic required study meta file, much like how we'd create a new R package and put a DESCRIPTION file in it.

Usage

cbp_new_study(
  cancer_study_identifier,
  name,
  type_of_cancer,
  description =
    "The data are contributed by researchers funded by the Neurofibromatosis Therapeutic Acceleration Program (NTAP). The reprocessing of the raw data is managed by the NF Open Science Initiative (https://nf.synapse.org/).",
  short_name = NULL,
  citation = NULL,
  pmid = NULL,
  groups = "PUBLIC",
  add_global_case_list = TRUE,
  validate = TRUE,
  verbose = TRUE
)

Arguments

cancer_study_identifier: Cancer study identifier in format such as nst_nfosi_ntap_2022.
name: Name of the study, e.g. "Malignant Peripheral Nerve Sheath Tumor (NF-OSI, 2022)".
type_of_cancer: Id for type of cancer. If validate is TRUE, this is one of the things validated with warning if mismatched.
description: Description of the study, defaults to a generic description that can be edited later.
short_name: (Optional) Short name for the study.
citation: (Optional) A relevant citation, e.g. "TCGA, Nature 2012".
pmid: (Optional) One or more relevant pubmed ids (comma-separated, no whitespace); if used, citation cannot be NULL.
groups: (Optional) Defaults to "PUBLIC" for use with public cBioPortal; otherwise, use group names that makes sense with the configuration of your cBioPortal instance.
add_global_case_list: (Optional) Use NULL to ignore, default is TRUE for an "All samples" case list( to be generated automatically.
validate: Validate against public cBioPortal configuration. Default TRUE, but might want to set to FALSE especially if using a custom cBioPortal instance with different configuration.
verbose: Whether to be chatty.