multiOmicsSurvivalModuleTest: Compute Multi Omics Survival in Pathway Modules

Description Usage Arguments Value

Description

Performs survival analysis using an 'Omics' object. The pathway (graph) used is decomposed in modules (cliques) using graph theory.

Usage

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multiOmicsSurvivalModuleTest(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" [email protected] is used as title

robust

should be used the robust mode for cox

include_from_annot

compute cox using additional covariates from annot

Value

MultiOmicsModules object


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