genlung {Ball}R Documentation

Lung cancer genomic data

Description

Publicly available lung cancer genomic data from the Chemores Cohort Study, containing the expression levels of mRNA, miRNA, artificial noise variables as well as clinical variables and response.

Format

genlung$survival: A data.frame containing n=123 complete observations. The first column is disease-free survival time and the second column is censoring status.

genlung$covariate: A data.frame containing p=2000 covariates.

Details

Tissue samples were analysed from a cohort of 123 patients, who underwent complete surgical resection at the Institut Mutualiste Montsouris (Paris, France) between 30 January 2002 and 26 June 2006. The studied outcome was the "Disease-Free Survival Time". Patients were followed until the first relapse occurred or administrative censoring. In this genomic dataset, the expression levels of Agilent miRNA probes (p=939) were included from the n=123 cohort samples. The miRNA data contains normalized expression levels. See below the paper by Lazar et al. (2013) and Array Express data repository for the complete description of the samples, tissue preparation, Agilent array technology, and data normalization. In addition to the genomic data, five clinical variables, also evaluated on the cohort samples, are included as continuous variable ('Age') and nominal variables ('Type','KRAS.status','EGFR.status','P53.status'). See Lazar et al. (2013) for more details. Moreover, we add 1056 standard gaussian variables which are independent with the censored response as noise covariates. This dataset represents a situation where the number of covariates dominates the number of complete observations or p >> n case.

References

Lazar V. et al. (2013). Integrated molecular portrait of non-small cell lung cancers. BMC Medical Genomics 6:53-65.


[Package Ball version 1.3.12 Index]