smoothCoxph: Plots the Cox proportional hazard smoothed by gene expression...

In phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

Description

Builds a plot showing how hazard behaves over different levels of expression of a given gene. Confidence intervals are also provided.

Usage

smoothCoxph(time, event, x, xlim, ylim, xlab, ylab, logrisk=TRUE, ...)

Arguments

time	variable where time to survival is stored.
event	variable where survival event is stored.
x	numeric containing the expression levels of a given gene.
xlim	xlim for the plot.
ylim	ylim for the plot.
xlab	xlab for the plot.
ylab	ylab for the plot.
logrisk	logrisk if we want to compute risk or logrisk estimates. By default this is TRUE, which has a better behaviour under small sample sizes.
...	other arguments that will be passed to plot.

Author(s)

David Rossell.

Examples

#load eset
data(eset)

#make plot
smoothCoxph(pData(eset)$Months2Relapse,pData(eset)$Relapse,exprs(eset)[25,])

phenoTest documentation built on Nov. 8, 2020, 7:53 p.m.