guessInvolvementPathway: Guess the most influent features from MultiOmics Survival...

In cavei/MOSClip: Multi Omics Survival Clip

Description

Given a pathway analyzed by MultiOmicsPathwaySurvivalTest it retrieve for each omic the most influent fetures.

Usage

guessInvolvementPathway(pathway, loadThr = 0.6, n = 3, atleast = 1,
  min_prop_pca = 0.1, min_prop_events = 0.1)

Arguments

pathway	MultiOmicsPathway from a pathway.
loadThr	the leading threshold to select genes (PCA only)
n	the maximum number of genes to retrive (cluster and binary only)
atleast	the minimum number of features to select (PCA only)
min_prop_pca	the minimal proportion to compute the pca classes
min_prop_events	the minimal proportion to compute the event classes

Value

For each omic analyzed a list that is the summary for omic summarized using the setted method: pvalues are present only for cluster method.

sigModule	the original data for significant features
discrete	the discrete version of the significant covariates converted (when needed) into the discrete version
subset	data.frame(row.names=names(topGenes), metClust=topGenes)
pvalues	Kruskal Wallis pvalues of the selected features
covsConsidered	the name of the considered omic

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