GeneCovMB: Data from the Parsons et al. 2011 study: Total number of...
In CancerMutationAnalysis: Cancer mutation analysis
Description
Usage
Format
References
See Also
Description
Total numbers of nucleotides "at risk" that were
successfully sequenced in RefSeq genes in the Parsons et al. 2011
medulloblastoma (MB) study.
Usage
1
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
CancerMutationAnalysis documentation built on Nov. 8, 2020, 6:47 p.m.
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Description Usage Format References See Also
Description
Total numbers of nucleotides "at risk" that were successfully sequenced in RefSeq genes in the Parsons et al. 2011 medulloblastoma (MB) study.
Usage
1 | 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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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