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Last data update: 2014.03.03

R: A filter function for univariate Cox regression.

coxfilter

R Documentation

A filter function for univariate Cox regression.

Description

A function that performs Cox regression with bindings for surt, cens, and p is returned. This function filters genes according to the attained p-value from a Cox regression using surt as the survival times, and cens as the censoring indicator. It requires survival.

Usage

coxfilter(surt, cens, p)

Arguments

`surt`	Survival times.
`cens`	Censoring indicator.
`p`	The p-value to use in filtering.

Value

Calls to the coxph function in the survival library are used to fit a Cox model. The filter function returns TRUE if the p-value in the fit is less than p.

Author(s)

R. Gentleman

Examples

   set.seed(-5)
   sfun <- coxfilter(rexp(10), ifelse(runif(10) < .7, 1, 0), .05)
   ffun <- filterfun(sfun)
   dat <- matrix(rnorm(1000), ncol=10)
   out <- genefilter(dat, ffun)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(genefilter)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genefilter/coxfilter.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coxfilter
> ### Title: A filter function for univariate Cox regression.
> ### Aliases: coxfilter
> ### Keywords: manip
> 
> ### ** Examples
> 
>    set.seed(-5)
>    sfun <- coxfilter(rexp(10), ifelse(runif(10) < .7, 1, 0), .05)
>    ffun <- filterfun(sfun)
>    dat <- matrix(rnorm(1000), ncol=10)
>    out <- genefilter(dat, ffun)
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
Error in eval(expr, envir, enclos) : could not find function "Surv"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>