read_rnaseq: Reads Level 3 RNA sequencing data from GDC.

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

Description

Reads RNASeq Level 3 data downloaded from GDC. The functions does some conservative checking in order to validate that all samples and features are annotated correctly. Also note that duplicate data (files with the same extract name) will be treated as independent duplicates for the same sample.

Usage

read_rnaseq(manifest, folder, normalization = "counts", progress = TRUE)

Arguments

manifest	Path to the GDC file manifest.
folder	Folder where the data files reside.
normalization	The normalization method. Must be one of "counts" The raw counts. "FPKM" Fragments Per Kilobase of transcript per Million mapped reads. "FPKM-UQ" Fragments Per Kilobase of transcript per Million mapped reads with Upper Quartile normlization.
progress	Logical. Show progress info?

Value

A data table containing the features as rows and the samples in the columns.

See Also

read_rnaseq_legacy to read legacy data.

Examples

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

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