GeneAlterGBM: Data from the Parsons et al. 2008 study: Alterations for...

In CancerMutationAnalysis: Cancer mutation analysis

Description

Somatic alterations for each gene and tumor sample from the Parsons et al. 2008 glioblastoma multiforme (GBM) study.

Usage

data(ParsonsGBM08)

Format

The somatic mutations in the GBM study from Parsons et al., broken down by gene, type (point mutation, amplification, or deletion), sample, screen (Discovery or Prevalence), and, for point mutations, mutation type, composed of the wild type nucleotide, its context, and the mutated nucleotide. The object is a data frame, with the variables: Gene, Type, Sample, Screen, WTNuc (wild type nucleotide), Context, and MutNuc (mutated nucleotide). The two possible values for Screen are Disc ("Discovery") and Prev ("Prevalence"). For this study, only the Discovery screen is considered. The three possible values for Type are Mut (point mutations), Amp (large amplifications), and Del (large deletions.) Indels have a "" entry for WTNuc, an "All" entry for Context, and a "ins.del" entry for MutNuc. Large amplifications and deletions have "" entries for WTNuc, Context, and MutNuc.

References

Parsons DW, Jones S, Zhang X, Lin JCH, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu I, et al. An integrated genomic analysis of human glioblastoma multiforme. Science. DOI: 10.1126/science.1164382

Parmigiani G, Lin J, Boca S, Sjoeblom T, Kinzler KW, Velculescu VE, Vogelstein B. Statistical methods for the analysis of cancer genome sequencing data. http://www.bepress.com/jhubiostat/paper126/

See Also

cma.scores, cma.fdr, cma.set.stat, cma.set.sim, SimMethodsSims-class, GeneCovGBM, GeneSampGBM

CancerMutationAnalysis documentation built on Nov. 8, 2020, 6:47 p.m.