cbp_add_expression: Export and add expression data to cBioPortal dataset

In nf-osi/nfportalutils: NF Portal Utilities

Export and add expression data to cBioPortal dataset

Description

This should be run in an existing dataset package root. Note that there are a number of different options generated by the STAR Salmon pipeline. cBioPortal has confirmed that they prefer normalized counts gene_tpm.tsv.

Usage

cbp_add_expression(expression_data, expression_data_raw = NULL, verbose = TRUE)

Arguments

expression_data	Syn id of normalized gene counts results (default to TPM). See details.
expression_data_raw	(Optional) Syn id of raw counts if curators explicitly ask for it.
verbose	Whether to be chatty.

nf-osi/nfportalutils documentation built on June 10, 2025, 5:08 a.m.