make_meta_genomic_generic: Generic template for genomic-type data file

In nf-osi/nfportalutils: NF Portal Utilities

Generic template for genomic-type data file

Description

Adapted from https://github.com/Sage-Bionetworks/genie-erbb2-cbio/blob/develop/make_meta.R#L65 Internal workhorse union of all the properties used for a genomic-type data file – the sensible defaults/specific combination should be passed in by a higher-level fun, e.g. make_meta_maf.

Usage

make_meta_genomic_generic(
  cancer_study_identifier,
  genetic_alteration_type,
  datatype,
  stable_id = NULL,
  reference_genome_id = NULL,
  profile_name = NULL,
  profile_description = NULL,
  data_filename
)

Arguments

cancer_study_identifier	The study identifier.
genetic_alteration_type	The cBioPortal generic alteration type.
datatype	The cBioPortal data type of data_filename.
stable_id	Stable id.
reference_genome_id	Reference genome id, e.g. 'hg19'.
profile_name	Name of the genomic profiling. This is set by the more specific make_meta utility. For example, "Mutations" for ⁠make_*_maf⁠ and "Copy-number alterations" for ⁠make_*_cna⁠.
profile_description	Brief description for the genomic profiling. This is set by the more specific make_meta utility.
data_filename	Name of the data file that this meta file describes.

nf-osi/nfportalutils documentation built on Feb. 26, 2024, 1:05 p.m.