GeneAlterBreast: Data from the Wood et al. 2007 and Sjoeblom et al. 2006...

In CancerMutationAnalysis: Cancer mutation analysis

Description

Somatic alterations for each gene and tumor sample from the breast cancer portion of the Wood et al. 2007 and Sjoeblom et al. 2006 studies.

Usage

data(WoodBreast07)

Format

The somatic mutations in the breast cancer portions of the Wood et al. and Sjoeblom et al. studies, 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"). 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. For this study, only point mutation are available.

References

Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, et al. The genomic landscapes of human breast and colorectal cancers. Science. DOI:10.1126/science.1145720

Sjoeblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber T, Mandelker D, Leary R, Ptak J, Silliman N, et al. The consensus coding sequences of human breast and colorectal cancers. Science. DOI: 10.1126/science.1133427

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, GeneCovBreast, GeneSampBreast

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