allHR: For all possible separation points for a cohort ordered by a...

In pearcedom/srvALL: Continuous Biomarker Assessment by Exhaustive Survival Analysis

Description

For all possible separation points for a cohort ordered by a continuous measurement, calculate hazard ratio

Usage

allHR(measure, srv, time = "Time", event = "Event", log2HR = TRUE,
  remove_outliers = TRUE)

Arguments

measure	A continuous variable used to order survival data. Samples must be ordered exactly as in srv
srv	A dataframe that contains at least two columns, detailing event and time to event information. Samples must be ordered exactly as in measure
time	Column name in srv containing time to event information. Must not contain NAs
event	Column name in srv containing event information coded as 0 (no event) and 1 (event). Must not contain NAs
log2HR	Hazard ratios are returned as log2 values by default
remove_outliers	Large hazard ratios result from statistical disproportion when considering edge cases (e.g. 1 vs 99) and can be automaticall removed

Value

A vector of hazard ratios calculated from srv ordered by measure

Examples

library(survivALL)
data(nki_subset)
library(Biobase)
gene_vec <- exprs(nki_subset)["NM_004448", ] #ERBB2 gene id
allHR(measure = gene_vec, srv = pData(nki_subset), time = "t.dmfs", 
    event = "e.dmfs", log2HR = TRUE)

pearcedom/srvALL documentation built on May 24, 2019, 2:49 p.m.