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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.