cbp_new_study: Initialize a new cBioPortal study dataset
In nf-osi/nfportalutils: NF Portal Utilities

cbp_new_study

R Documentation

Initialize a new cBioPortal study dataset

Description

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.