ExposureSurvival: Exposure survival analysis

In rvalieris/signeR: Empirical Bayesian approach to mutational signature discovery

Exposure survival analysis

Description

ExposureSurvival: Given survival data, identify signatures that are significantly related to differences in hazards.

Usage

## S4 method for signature 'SignExp,Surv'
ExposureSurvival(signexp_obj, surv, max_instances=200,
    method=logrank, quant=0.5, cutoff_pvalue=0.05, cutoff_hr=NA,
    plot_to_file=FALSE, file="ExposureSurvival_plot.pdf",
    colors=TRUE, ...)

Arguments

signexp_obj	a SignExp object returned by signeR function.
surv	a Surv object from package survival or a matrix with columns "time" and "status" (the last indicates whether 1:an event occurred or 0:there was a loss of follow up).
max_instances	Maximum number of the exposure matrix instances to be analyzed. If the number of available E instances is bigger than this parameter, a subset of those will be randomly selected for analysis.
method	a character string indicating which approach should be used for the test. Options are "logrank" (default) or "cox" (fit a Cox proportional hazards model to data).
quant	the quantile of p-values and hazard ratios which will be used for selecting survival significant signatures. Default is 0.5, which means the median p-value and hazard ratio will be considered.
cutoff_pvalue	threshold for p-values quantile for signatures to be considered as significant.
cutoff_hr	threshold for hazard ratio quantile for signatures to be considered as significant.
plot_to_file	Whether to save the plot to the file parameter. Default is FALSE.
file	Output file to export p-values boxplots and Kaplan-Meier curves.
colors	Boolean variable, if TRUE p-values boxplots of significant signatures will be colored in green, cutoff line will be colored in red and line segments showing the transformed p-value quantile used for significance evaluation will be colored in blue. Otherwise the plot will be black & white.
...	additional parameters for test algorithm defined by the method parameter.

Value

A list with the following items:

Significance	boolean array with one entry for each signature, indicating whether its levels of exposure are significant to survival.
Correlation_quantiles	vector of correlation quantiles, with one entry for each signature.
pvalues	vector of p-values used for significance evaluation.
limits	vector containing one cut value for the exposures of each signature, such that splitting the samples according to this value leads to maximal differences in survival among generated groups.
Groups	matrix containing one line for each signature, defining a division of the samples into two groups according to their exposures, such that survival differences between the groups are maximal.

Examples

# assuming signatures is the return value of signeR()

# feature vector, with one value for each sample
library(survival)
my_surv <- Surv(rnorm(30,730,100),sample(c(0:1),30,replace=TRUE))

Exp_corr <- ExposureSurvival(signatures$SignExposures, surv = my_surv)

# see also
vignette(package="signeR")

rvalieris/signeR documentation built on April 20, 2024, 2:08 p.m.