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

In dongjunchung/PICS: PICS (Pathway-guided Identification of Cancer Subgroups)

Description

An S4 class for pathway-level analysis results

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

dongjunchung/PICS documentation built on May 15, 2019, 10:39 a.m.