survivALL
Continuous Biomarker Assessment by Exhaustive Survival Analysis

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survivALL: Calculate and combine hazard ratio, pvalue, threshold and...

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

Description Usage Arguments Value Examples

View source: R/survivALL.R

Description

Calculate and combine hazard ratio, pvalue, threshold and area-between-curve data as a single dataframe

Usage

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survivALL(measure, srv, time = "Time", event = "Event", bs_dfr = c(),
  measure_name = "measure", multiv = NULL, n_sd = 1.96,
  remove_outliers = TRUE)

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

n_sd

The number of standard deviations used to define threshold width. 95 deviation of 1.96

remove_outliers

Large hazard ratios result from statistical disproportion when considering edge cases (e.g. 1 vs 99) and can be automaticall removed

Value

a dataframe detailing survival, measure, hazard ratio, pvalue, log10 pvalue, threshold and threshold residual information

Examples

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library(survivALL)
data(nki_subset)
library(Biobase)
library(ggplot2)

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

survivALL_dfr <- survivALL(measure = gene_vec, 
   srv = pData(nki_subset), 
   time = "t.dmfs", 
   event = "e.dmfs")

ggplot(survivALL_dfr, aes_string(x = 'measure', y = 'p')) + 
    geom_hline(yintercept = 0.05, linetype = 3) + 
    geom_point()

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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Warning message:
In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
Warning message:
Removed 1 rows containing missing values (geom_point).

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

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