write_cbio_clinical: Write cBioPortal clinical file
In nf-osi/nfportalutils: NF Portal Utilities

write_cbio_clinical

R Documentation

Write cBioPortal clinical file

Description

Wrapper function for creating clinical files. There are two: PATIENT and SAMPLE. The PATIENT file is actually optional, so there are only checks for making sure SAMPLE can be created. df is expected to be a table containing clinical data available, and maybe even some irrelevant data (since NF data is not well-normalized and there is a single table with everything).

Usage

write_cbio_clinical(
  df,
  ref_map,
  na_recode = c("NA", "NaN", "unknown", "Unknown"),
  delim = "\t",
  publish_dir = ".",
  verbose = TRUE
)

Arguments

`df`	A `data.frame` representing clinical dataset to publicize.
`ref_map`	YAML or JSON mapping. See details.
`na_recode`	Possible NA values to replace with a blank string (which seems to be standard) in exported file.
`delim`	Delimiter character used for writing file, defaults to tab-delimited per cBioPortal specs.
`publish_dir`	Directory path to write to, defaults to current.
`verbose`	Report where file has been written.

Details

This depends on a ref_map specification to know which clinical data to include for cBioPortal and how to segregate the clinical attributes into the right files. Basically, ref_map decides what variables can be made public and how they should be represented in cBioPortal. For example, given a table T on Synapse with variables A-Z and mappings in ref_map for A-C + L-M, we take the intersection of variables present. But first, check that required variables in ref_map are present. So first the subset df is created from T.