templates.CMS: development consensus molecular subtype (CMS) templates

In peterawe/CMScaller: CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Description

development consensus molecular subtype (CMS) templates

Usage

templates.CMS

Format

An object of class data.frame with 530 rows and 3 columns.

Details

Colorectal cancer Consensus Molecular Subtypes (CMS) prediction templates for ntp. Marker genes were identified using TCGA RNA-sequencing data. templates$probe refers to Entrez ids. Compared to templates.CMS this was prepared using additional filters steps to further clean genes also expressed by non-carcinoma cell types. Predictions are usually highly concordant with templates.CMS. Under development.

References

Guinney J, Dienstmann R, Wang X, de Reynies A, Schlicker A, Soneson C, et al. The consensus molecular subtypes of colorectal cancer. Nat Med [Internet]. 2015 [cited 2015 Nov 5];advance online publication. Available from: http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3967.html

Hoshida Y. Nearest Template Prediction: A Single-Sample-Based Flexible Class Prediction with Confidence Assessment. PLoS ONE. 2010;5:e15543.

Examples

length(intersect(templates.CMS$symbol, templates.CMS$symbol))
length(setdiff(templates.CMS$symbol, templates.CMS$symbol))

peterawe/CMScaller documentation built on June 13, 2020, 4:49 a.m.