calculateSurvival: Given alternate promoter score for samples, divide samples...

In aditiqamra/APcalc: Calculate APscore

Description

Given alternate promoter score for samples, divide samples into groups and calculate survival differences

Usage

calculateSurvival(alternatePromoterScore, clinicaldata,
  alternatePromoterQuantileThreshold, survivalTime, survivalEvent, title,
  ...)

Arguments

alternatePromoterScore	A data.frame object. Two columns containing sample ids and numeric alternate promoter score
clinicaldata	A data.frame object. Should have an id column labelled "id" and have survival time and event information
survivalTime	Column in clinicaldata specifying survival time
survivalEvent	Column in clinicaldata specifying event information
title	Character type. Label to plot on survival curve
alternatePromoterUpperQuantileThreshold	Numeric value greater than 0 and less than 1. Identifying threshold to define samples into APhigh and APlow. APhigh samples will be alternatePromoterScore >= quantile(alternatePromoterScore,alternatePromoterUpperQuantileThreshold). APlow samples will be alternatePromoterScore <= quantile(alternatePromoterScore,(1-alternatePromoterUpperQuantileThreshold)).

Value

A data.frame object. Return alternatePromoterScore with AP group classification

See Also

calculateAlternatePromoterScore for calculating alternate promoter score for samples

Examples

## Not run: 
alternatePromoterGroups <- calculateSurvival(alternatePromoterScore,
                                                         clinicaldata,
                                                         alternatePromoterUpperQuantileThreshold=0.66,
                                                         survivalTime="pfs",
                                                         survivalEvent="progression",
                                                         title="AP Group -  66/33 Split")

## End(Not run)

aditiqamra/APcalc documentation built on Jan. 23, 2020, 4:39 p.m.