Setup Expression Data (cBioPortal). — setup_expreession

Generate expression data based on a set of genes, format and export data for cBioPortal.

setup_expreession_data(
  project_name = "gambl_genome",
  clinical_file_path = "data_clinical_samples.txt",
  these_genes,
  expression_df,
  out_dir
)

Arguments

project_name: Unique ID for your project.
clinical_file_path: The path to the study specific clinical file (data_clinical_samples.txt).
these_genes: Specify a set of genes (character of vectors) that you want to return expression data for. If no genes are provided, this function will resort to all lymphoma genes.
expression_df: Optional argument for providing an already loaded expression matrix.
out_dir: The full path to the base directory where the files are being created.

Value

A vector of characters with sample IDs that expression data was generated for.

Details

This function takes a set of genes with the these_genes (character of vectors) parameter and returns expression data. Expression data is then formatted to match the expected format for import to a cBioPortal study. If no genes are provided, the function will default to all genes that are defined in the lymphoma_genes bundled data. This function internally calls get_gene_expression for returning expression data as outlined above.

Examples

if (FALSE) {
#return expression data for lymphoma genes (all samples)
expression_ids = setup_expression_data(out_dir = "../../")
}