template.CMS.A: Mouse CMS template (option A)
In MolecularPathologyLab/MmCMS: Calling CMS for mouse tissue
template.CMS.A R Documentation
Mouse CMS template (option A)
Description
Mouse CMS template (option A)
Usage
template.CMS.A
Format
An object of class data.frame with 424 rows and 2 columns.
Details
CMS prediction template for NTP method. Marker genes were
identified by converting human CMS template from CMScaller to mouse orthologe using biomaRt.
templates$probe refers to gene symbols.
References
Eide PW, Bruun J, Lothe RA, Sveen A. CMScaller:
an R package for consensus molecular subtyping of colorectal cancer pre-clinical models. Scientific reports (2017)
Guinney J, Dienstmann R, Wang X, de Reynies A, Schlicker A, Soneson C, et al. The consensus molecular subtypes of colorectal cancer. Nat Med (2015)
Hoshida Y. Nearest Template Prediction: A Single-Sample-Based Flexible Class Prediction with Confidence Assessment. PLoS ONE (2010)
Durinck S, Spellman P, Birney E, Huber W (2009). “Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.” Nature Protocols, 4, 1184–1191.
Examples
emat <- TestData_gemm
re <- MmCMS(emat, templates=MmCMS::template.CMS.A, Genesets = c("template.CMS.A"), seed=120)
MolecularPathologyLab/MmCMS documentation built on Oct. 18, 2023, 10:42 p.m.
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| template.CMS.A | R Documentation |
Mouse CMS template (option A)
Description
Mouse CMS template (option A)
Usage
template.CMS.A
Format
An object of class data.frame with 424 rows and 2 columns.
Details
CMS prediction template for NTP method. Marker genes were
identified by converting human CMS template from CMScaller to mouse orthologe using biomaRt.
templates$probe refers to gene symbols.
References
Eide PW, Bruun J, Lothe RA, Sveen A. CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models. Scientific reports (2017)
Guinney J, Dienstmann R, Wang X, de Reynies A, Schlicker A, Soneson C, et al. The consensus molecular subtypes of colorectal cancer. Nat Med (2015)
Hoshida Y. Nearest Template Prediction: A Single-Sample-Based Flexible Class Prediction with Confidence Assessment. PLoS ONE (2010)
Durinck S, Spellman P, Birney E, Huber W (2009). “Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.” Nature Protocols, 4, 1184–1191.
Examples
emat <- TestData_gemm
re <- MmCMS(emat, templates=MmCMS::template.CMS.A, Genesets = c("template.CMS.A"), seed=120)
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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