GeneCovMB {CancerMutationAnalysis} | R Documentation

## Data from the Parsons et al. 2011 study: Total number of nucleotides "at risk" ("coverage")

### Description

Total numbers of nucleotides "at risk" that were successfully sequenced in RefSeq genes in the Parsons et al. 2011 medulloblastoma (MB) study.

### Usage

    data(ParsonsMB11)

### Format

Total number of nucleotides available for mutations ("coverage") in the MB study from Parsons et al., broken down by gene, screen (Discovery or Prevalence), and mutation type, composed of the wild type nucleotide and its context. The object is a data frame, with the variables: Gene, Screen, WTNuc (wild type nucleotide), Context, and Coverage. The two possible values for Screen are Disc ("Discovery") and Prev ("Prevalence"). The nucleotides availables for indels are all the successfully sequenced nucleotides in a gene; the corresponding rows have a "" entry for WTNuc and an "All" entry for "Context." The nucleotides availables for other mutations are excluding nucleotides which can only give rise to synonymous mutations.

### References

Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin J, Boca SM, Carter H, Samayoa J, Bettegowda C, et al. The genetic landscape of the childhood cancer medulloblastoma. Science. DOI: 10.1126/science.1198056

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`, `GeneAlterMB`, `GeneSampMB`

[Package CancerMutationAnalysis version 1.28.0 Index]