MmCMS: CMS classification

In MolecularPathologyLab/MmCMS: Calling CMS for mouse tissue

CMS classification

Description

consensus molecular subtypes (CMS) classification for mouse tissues.

Usage

MmCMS(
  emat,
  templates = MmCMS::template.CMS.A,
  Genesets = c("template.CMS.B", "template.CMS.C", "template.CMS.A"),
  nPerm = 1000,
  seed = NULL,
  FDR = 0.05,
  doPlot = TRUE,
  verbose = TRUE
)

Arguments

emat	a numeric expression matrix with sample columns, and HGNC symbol rownames. Data should be normalized. see the example in TestData_gemm.
templates	a data frame with two columns; class (coerced to factor) and probe (coerced to character). There are 3 templates: 'template.CMS.A', 'template.CMS.B' and 'template.CMS.C'. Default is template.CMS.A
Genesets	Select the same as template
nPerm	an integer, number of permutations for p-value estimation.
seed	an integer, for p-value reproducibility.
FDR	a false discovery rate, sets prediction confidence threshold.
doPlot	a logical, whether to produce prediction subHeatmap.
verbose	a logical, whether console messages are to be displayed.

Details

MmCMS provides 3 options to call CMS subtypes in mouse tissues. The core algorithm is the CMScaller developed by Eide PW, et al. (2017) and the Nearest Template Prediction (NTP) algorithm as proposed by Yujin Hoshida (2010).

Value

a data frame with class predictions, template distances, p-values and false discovery rate adjusted p-values (p.adjust). Rownames equal emat colnames.

Note

genes with missing values are discarded.

References

Eide PW, Bruun J, Lothe RA, Sveen A. (2017). CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models. doi: 10.1038/s41598-017-16747-x.

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

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;21:1350-6.

See Also

template.CMS.A, template.CMS.B, template.CMS.C

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.