read_huex: Reads HuEx 1.0 st v2 exon expression data.

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

Description

This reads level 3 data for exon expression data.

Usage

read_huex(manifest, folder, features = "genes", progress = TRUE)

Arguments

manifest	Path to the GDC file manifest.
folder	Location of the directory containing downloaded TCGA data.
features	Which features to use. Can be either "genes" or "exons".
progress	Whether to show progress information.

Value

A list with three elements, a matrix of log-expression values, a data table giving additional information for samples and a data table describing the features (genes or exon IDs).

See Also

read_rnaseq to read RNASeq data.

Examples

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

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