TCGA-ESCA {plasma}

Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).

Description

The TCGA-ESCA dataset contains the objects assemble, Outcome, and m450info for building the MultiOmics object. Because its size exceeds the CRAN limits, the data is stored on a remote server and must be loaded using the function loadESCAdata.

The TCGA-LUSC1dataset is a parallel object for lung squamous cell carcinoma (LUSC) data, whihc must be loaded using the loadLUSCdata function.

Usage

loadESCAdata(env = plasmaEnv)
loadLUSCdata(env = plasmaEnv)

Arguments

env

an environment in which to load the data. The default value is a private environment in the package, accessible as plasmaEnv. To make access easier, you can use globalenv() or .GlobalEnv.

Format

The “TCGA-ESCA” dataset contains the following:

assemble

A list of 7 different omics dataframes with varying numbers of features as rows (D) and varying number of patients as columns (N). Note that some of these omics dataframes had been manipulated to contain NAs, where these may be complete on the GDC Dat Portal from which these data originally came. This was done to illustrate the capability of the plasma package on working with missing data.

ClinicalBin

a dataframe (53x185) of clinical binary values.

ClinicalCont

a dataframe (6x185) of clinical continuous values.

MAF

a dataframe (566x184) of minor allele frequencies (MAF) that have been converted to binary based on whether they had a MAF greater than 0.03 (1) or not (0).

Meth450

a dataframe (1454x185) of continuous beta values from the Illumina Infinium HumanMethylation450 arrays. The features in this dataframe have been filtered on mean greater than 0.15 and a standard deviation greater than 0.3.

miRSeq

a dataframe (926x166) of continuous counts values from microRNA (miRNA) sequencing. The features in this dataframe have been filtered on a standard deviation of 0.05.

mRNASeq

a dataframe (2520x157) of continuous counts values from mRNA sequencing data. The features in this dataframe have been filtered on a mean greater than 4 and a standard deviation greater than 0.7.

RPPA

a dataframe (192x126) of continuous protein expression values from reverse phase protein array (RPPA) assays.

Outcome

a dataframe (185x5) containing the survival outcomes for the patients in assemble.

m450info

a dataframe (1454x3) containing gene symbol, chromosome number, and genomic coordinate IDs corresponding to the features (or “probes”) in Meth450.

Author(s)

Kevin R. Coombes [e-mail], Kyoko Yamaguchi [e-mail]

Source

https://portal.gdc.cancer.gov/projects/TCGA-ESCA

Examples

fls <- try(loadESCAdata())
if (inherits(fls, "try-error")) {
  stop("Unable to load data from remote server.")
}