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.
use_rna_luad(userdir = "")
| userdir | the name of the folder to install the datasets. A temporary file will be used if left blank. |
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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.
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
if (FALSE) { 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 }