survivALL (version 0.9.3)

plotALL: Calculate and combine hazard ratio, pvalue, threshold and area-between-curve data and plot

Description

Calculate and combine hazard ratio, pvalue, threshold and area-between-curve data and plot

Usage

plotALL(measure, srv, time = "Time", event = "Event", bs_dfr = c(),
  measure_name = "measure", multiv = NULL, title = "")

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

title

Plot title; as a character string

Value

Using survival, measure, hazard ratio, pvalue, log10 pvalue, threshold and threshold residual information, plot the measure-event relationship

Examples

# NOT RUN {
data(nki_subset)
library(Biobase)

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

plotALL(measure = gene_vec, 
    srv = pData(nki_subset), 
    time = "t.dmfs", 
    event = "e.dmfs", 
    title = "ERBB2 Example") 

# }