CancerMutationAnalysis (version 1.14.0)

GeneCovColon: Data from the Wood et al. 2007 and Sjoeblom et al. 2006 studies: Total number of nucleotides "at risk" ("coverage")

Description

Total numbers of nucleotides "at risk" that were successfully sequenced in RefSeq genes in the colon cancer portion of the Wood et al. 2007 and Sjoeblom et al. 2006 studies.

Usage

data(WoodColon07)

Format

Total number of nucleotides available for mutations ("coverage") in the colon cancer portion of the Wood et al. and Sjoeblom et al. studies, 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

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 WK, 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, GeneAlterColon, GeneSampColon