allPvals: For all possible separation points for a cohort ordered by a...
In survivALL: Continuous Biomarker Assessment by Exhaustive Survival Analysis

Description Usage Arguments Value Examples

For all possible separation points for a cohort ordered by a continuous measurement, perform a uni- or multivariate log-rank test

1 2	allPvals(measure, srv, time = "Time", event = "Event", multiv = NULL, statistic = "logtest")

`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
`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
`statistic`	the statistical test to be used to compute significance. one of "logtest" (likelihood ratio test), "waldtest" (wald statistic) or "sctest" (log-rank test)

A vector of pvalues calculated from srv ordered by measure

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

allPvals(measure = gene_vec, 
    srv = pData(nki_subset), 
    time = "t.dmfs", 
    event = "e.dmfs",
    statistic = "logtest")


allPvals(measure = gene_vec, 
    srv = pData(nki_subset), 
    time = "t.dmfs", 
    event = "e.dmfs",
    multiv = "grade",
    statistic = "sctest")