multiOmicsSurvivalPathwayTest: Compute Multi Omics Survival in Pathways

In cavei/MOSClip: Multi Omics Survival Clip

Description

Performs topological survival analysis using an 'Omics' object.

Usage

multiOmicsSurvivalPathwayTest(omicsObj, graph, annot,
  survFormula = "Surv(days, status) ~", autoCompleteFormula = T,
  useThisGenes = NULL, pathName = NULL, robust = FALSE,
  include_from_annot = F)

Arguments

omicsObj	Object of class 'Omics'
graph	a pathway in graphNEL, Pathway or geneset format.
annot	survival annotation: days and status (0,1). Row.names are samples. Additional covariates can be passed as columns (use include_from_annot).
survFormula	Formula to compute survival
autoCompleteFormula	logical. If TRUE autocomplete the survFormula using all the available covariates
useThisGenes	vector of genes used to filter pathways
pathName	title of the pathway. If NULL and graph is "Pathway" graph@title is used as title
robust	should be used the robust mode for cox
include_from_annot	compute cox using additional covariates from annot

Value

MultiOmicsPathway object

cavei/MOSClip documentation built on May 12, 2019, 5:22 p.m.