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coxfilter: A filter function for univariate Cox regression.

coxfilter: A filter function for univariate Cox regression.
In genefilter: genefilter: methods for filtering genes from high-throughput experiments

Description Usage Arguments Value Author(s) See Also Examples

View source: R/all.R

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

1
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

See Also

Anova

Examples

1
2
3
4
5
   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)

Example output

Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"
Error in Surv(surt, cens) : could not find function "Surv"

genefilter documentation built on Jan. 23, 2021, 2:01 a.m.

Related to coxfilter in genefilter...

genefilter index
Additional plots for: Independent filtering increases power for detecting differentially expressed genes, Bourgon et al., PNAS (2010) How to find genes whose expression profile is similar to that of specified genes Using the genefilter function to filter genes from a microarray dataset

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