plotALL: Calculate and combine hazard ratio, pvalue, threshold and...
In survivALL: Continuous Biomarker Assessment by Exhaustive Survival Analysis

Description Usage Arguments Value Examples

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

1 2	plotALL(measure, srv, time = "Time", event = "Event", bs_dfr = c(), measure_name = "measure", multiv = NULL, title = "")

`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

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

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")