FitPath-class: An S4 class for pathway-level analysis results

In sunny-zq/INGRID: InGRiD: Semi-supervised Identification of Cancer Subgroups using Survival Outcomes and Overlapping Grouping Information

Description

Risk group prediction.

Plot Kaplan-Meier curves (type="KM"), ROC (type="ROC"), or hazard ratio (type="HR").

Usage

## S4 method for signature 'FitPath'
predict(object, newx = NULL, cuts = NULL)

## S4 method for signature 'FitPath,missing'
plot(x, y, type = "KM")

Arguments

object	output of selectPath function
newx	test gene expression data
cuts	cut points to determine risk groups
x	output of selectPath function
y	(unused argument)
type	type of plot. one of Kaplan-Meier curves (type="KM"), ROC (type="ROC"), or hazard ratio (type="HR").

Slots

PathAll

all pathways

PathSelected

pathways selected by LASSO

coef

LASSO coefficient estimates for pathway latent components

fitGene

gene-level analysis results

sunny-zq/INGRID documentation built on Oct. 15, 2019, 6:45 p.m.