use_rna_luad: Download a toy dataset to test galgoR

In harpomaxx/galgo: An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

Description

The current function downloads two reduced lung adenocarcinoma gene expression datasets (TCGA lung adenocarcinoma project and GEO GSE68465 datasets) to test galgoR. It also contains the Wilkerson's centroids to perform lung adenocarcinoma sample classification.

Usage

use_rna_luad(userdir = "")

Arguments

userdir

the name of the folder to install the datasets. A temporary file will be used if left blank.

Value

The dataset gets downloaded in a temporary folder or the userdir folder specified by the user. The output of the function is a list with two lists with the scaled gene expression and clinical data from TCGA lung adenocarcinoma and GEO GSE68465 datasets.It also contains the Wilkerson's centroids extracted from http://cancer.unc.edu/nhayes/publications/adenocarcinoma.2012/wilkerson.2012.LAD.predictor.centroids.csv.zip to perform sample classification into "Bronchoid", "Magnoid" and "Squamoid" subtypes.

References

• Shedden, K., Taylor, J., Enkemann, S. et al. Gene expression–based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 14, 822-827 (2008). https://doi.org/10.1038/nm.1790

• Collisson, E., Campbell, J., Brooks, A. et al. Comprehensive molecular profiling of lung adenocarcinoma. Nature 511, 543-550 (2014). https://doi.org/10.1038/nature13385

• Matthew D. Wilkerson, Xiaoying Yin, Katherine A. Hoadley, Yufeng Liu, Michele C. Hayward, Christopher R. Cabanski, Kenneth Muldrew, C. Ryan Miller, Scott H. Randell, Mark A. Socinski, Alden M. Parsons, William K. Funkhouser, Carrie B. Lee, Patrick J. Roberts, Leigh Thorne, Philip S. Bernard, Charles M. Perou and D. Neil Hayes. Clin Cancer Res October 1 2010 (16) (19) 4864-4875 https://doi.org/10.1158/1078-0432.CCR-10-0199

• Wilkerson MD, Yin X, Walter V, Zhao N, Cabanski CR, Hayward MC, et al. (2012) Differential Pathogenesis of Lung Adenocarcinoma Subtypes Involving Sequence Mutations, Copy Number, Chromosomal Instability, and Methylation. PLoS ONE 7(5): e36530. https://doi.org/10.1371/journal.pone.0036530

Examples

## Not run: 
rna_luad<- use_rna_luad()
TCGA<- rna_luad$TCGA #Access TCGA dataset
GSE68465<- rna_luad$GSE68465 #Access GSE68465 dataset

#To access gene expression data
TCGA_expr<- TCGA$expression_data

#To access feature data
TCGA_features<- TCGA$feature_data

#To access clinical data
TCGA_clinic <- TCGA$pheno_data

#To get wilkerson centroids
WilkCentroids <- rna_luad$WilkCentroids

## End(Not run)

harpomaxx/galgo documentation built on Aug. 11, 2020, 3:07 p.m.