GetSurvivalProbe: The GetSurvivalProbe function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The GetSurvivalProbe function

Description

Get probes whose methylation state is predictive of patient survival

Usage

GetSurvivalProbe(
  EpiMixResults,
  TCGA_CancerSite = NULL,
  clinical.data = NULL,
  raw.pval.threshold = 0.05,
  p.adjust.method = "none",
  adjusted.pval.threshold = 0.05,
  OutputRoot = ""
)

Arguments

EpiMixResults	List of objects returned from the EpiMix function
TCGA_CancerSite	String indicating the TCGA cancer code (e.g. 'LUAD')
clinical.data	(If the TCGA_CancerSite is specified, this parameter is optional) Dataframe with survival information. Must contain at least three columns: 'sample.id', 'days_to_death', 'days_to_last_follow_up'.
raw.pval.threshold	numeric value indicting the raw p value threshold for selecting the survival predictive probes. Survival time is compared by log-rank test. Default: 0.05
p.adjust.method	character string indicating the statistical method for adjusting multiple comparisons, can be either of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none'. Default: 'fdr'
adjusted.pval.threshold	numeric value indicting the adjusted p value threshold for selecting the survival predictive probes. Default: 0.05
OutputRoot	path to save the output. If not null, the return value will be saved as 'Survival)Probes.csv'.

Value

a dataframe with probes whose methylation state is predictive of patient survival and the p value.

Examples

library(survival)

data('Sample_EpiMixResults_miRNA')

survival.CpGs <- GetSurvivalProbe(EpiMixResults = Sample_EpiMixResults_miRNA,
                                     TCGA_CancerSite = 'LUAD')

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.