allHR |
For all possible separation points for a cohort ordered by a continuous measurement, calculate hazard ratio |
allPvals |
For all possible separation points for a cohort ordered by a continuous measurement, perform a uni- or multivariate log-rank test |
areaBetweenCurves |
Calculate the area above the bootstrapped thresholds but below the HR distribution and vice versa for each point of separation |
bootstrapThresholds |
Calculate per-separation point hazard ratio thresholds |
checkContSig |
Calculate association between survival and a continuous measure#' @inheritParams allPvals |
compSelect |
Given a dataframe of phenotypic information, use a variable (i.e. a single column) to define a patient subset of given proportion |
hrSignificance |
Calculate HR significance using bootstrap results |
nki_subset |
NKI breast cancer patients subset with complete t.dmfs and e.dmfs information |
plotALL |
Calculate and combine hazard ratio, pvalue, threshold and area-between-curve data and plot |
removeOutliers |
Calculate outliers in a numeric vector and then convert those values to NA |
survivALL |
Calculate and combine hazard ratio, pvalue, threshold and area-between-curve data as a single dataframe |