bootstrapThresholds: Calculate per-separation point hazard ratio thresholds

In survivALL: Continuous Biomarker Assessment by Exhaustive Survival Analysis

Description

Calculate per-separation point hazard ratio thresholds

Usage

bootstrapThresholds(bs_dfr, n_sd = 1.96)

Arguments

bs_dfr	A matrix of bootstrapped hazard ratio computations as ordered by a random measurement vector. Typically consisting of 5-10,000 repeat samplings
n_sd	The number of standard deviations used to define threshold width. 95 deviation of 1.96

Value

A dataframe of per-separation point mean, upper and lower thresholds

Examples

data(nki_subset)
library(Biobase)
library(magrittr)
library(ggplot2)

#simulate example HR bootstrapped data
bs_dfr <- matrix(rnorm(150000), ncol = 1000, nrow = 150)

#calculate thresholds
thresholds <- bootstrapThresholds(bs_dfr)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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survivALL documentation built on May 1, 2019, 11:02 p.m.