Data from the Jones et al. 2008 study: Alterations for every gene and sample

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Description

Somatic alterations for each gene and tumor sample from the Jones et al. 2008 pancreatic cancer study.

Usage

1
data(JonesPancreas08)

Format

The somatic mutations in the pancreatic cancer study from Jones 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

Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. DOI: 10.1126/science.1164368

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, GeneCovPancreas, GeneSampPancreas

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