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 and, though not used, find it helpful to also have raw counts gene_counts.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 results. See details.
verbose	Whether to be chatty.

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