read_clinical: Reads clinical data from TCGA for multiple samples.

In cdiener/tcgar: A small helper package for using data from the Genomic Data Commons

Description

This function assembles a data set with the major clinical indicators for each patient as well as sample procurement data for all the samples available for each patient from TCGA Biotab data.

Usage

read_clinical(manifest, folder, additional = NULL, progress = TRUE)

Arguments

manifest	Path to the GDC file manifest.
folder	The folder that contains the data.
additional	A named vector with entries 'name = xpath' where 'name' is the column name that should be extracted and 'xpath' is an XPath expression defining the XML tag that should be read. Entries will returned as unmodified strings.
progress	Whether to show progress information.

Value

A data table containing the information for patients on its rows.

Examples

# Not run due to large download...
# gbm <- system.file("extdata", "manifest.tsv", package = "tcgar")
# d <- tempdir()
# clin <- read_clinical(gbm, d)

cdiener/tcgar documentation built on May 13, 2019, 2:41 p.m.