survivALL: Calculate and combine hazard ratio, pvalue, threshold and...

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

Description

Calculate and combine hazard ratio, pvalue, threshold and area-between-curve data as a single dataframe

Usage

survivALL(measure, srv, time = "Time", event = "Event", bs_dfr = c(),
  measure_name = "measure", multiv = NULL, n_sd = 1.96,
  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
bs_dfr	A matrix of bootstrapped hazard ratio computations as ordered by a random measurement vector. Typically consisting of 5-10,000 repeat samplings
measure_name	A descriptive name for the measure used, for example a gene ID
multiv	Univariate analysis is performed by default, however a character string specifying a column contained in srv (or a vector of strings specifying multiple columns) detailing additional variables can be included
n_sd	The number of standard deviations used to define threshold width. 95 deviation of 1.96
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 dataframe detailing survival, measure, hazard ratio, pvalue, log10 pvalue, threshold and threshold residual information

Examples

library(survivALL)
data(nki_subset)
library(Biobase)
library(ggplot2)

gene_vec <- exprs(nki_subset)["NM_004448", ] #ERBB2 gene id

survivALL_dfr <- survivALL(measure = gene_vec, 
   srv = pData(nki_subset), 
   time = "t.dmfs", 
   event = "e.dmfs")

ggplot(survivALL_dfr, aes_string(x = 'measure', y = 'p')) + 
    geom_hline(yintercept = 0.05, linetype = 3) + 
    geom_point()

pearcedom/survivALL documentation built on May 20, 2019, 2:26 p.m.