DRLevelAnalysis: Caculate response evaluation indexes

In SCBIT-YYLab/DRAP: Drug Response Analysis Tailored for Drug Testing on Patient-Derived Tumor Models

Description

Caculate response evaluation indexes, such as RR and DCR, based on drug response level.

Usage

DRLevelAnalysis(data, by, measurement = c('RR','DCR','both'))

Arguments

data	drug response level ,the output of DRLevel.
by	the level summaried by.
measurement	the measurement of drug response criteria calcuated, whether "RR", "DCR", or "both".

Details

RR (response rate) is the percentage of animals that response level is better than partial repsone (PR) after treatment. DCR (decease control rate) is the percentage of animals that response level is better than stable disease (SD) after treatment.

Examples

# NPDXE.criteria 
npdxe.criteria <- data.frame(BestResponse.lower = c(-1000,-0.95,-0.5,0.35),
                             BestResponse.upper = c(-0.95,-0.5,0.35,1000),
                             BestAvgResponse.lower = c(-1000,-0.4,-0.2,0.3), 
                             BestAvgResponse.upper = c(-0.4,-0.2,0.3,1000), 
                             Level = c( 'CR','PR', 'SD','PD'))
npdxe.criteria

### oneAN pattern
data(oneAN.volume.data)
oneAN.drl <- DRLevel(data = oneAN.volume.data, method = 'NPDXE.Response', 
                     criteria = npdxe.criteria, neg.control = 'Control')
DRLevelAnalysis(oneAN.drl,by = 'Arms', measurement = 'both')


### TAN pattern
data(TAN.volume.data)
TAN.drl <- DRLevel(data = TAN.volume.data, method = 'NPDXE.Response', 
                   criteria = npdxe.criteria, neg.control = 'Control')
DRLevelAnalysis(TAN.drl,by='Arms',measurement = 'both')
DRLevelAnalysis(TAN.drl,by=c('Arms','Tumor'),measurement = 'both')

### TAone pattern
data(TAone.volume.data)
TAone.drl <- DRLevel(data = TAone.volume.data, method = 'NPDXE.Response', 
                     criteria = npdxe.criteria, neg.control = 'Control')
head(TAone.drl)
TAone.drl.analysis = DRLevelAnalysis(data = TAone.drl,by = c('Arms','Type'),measurement = 'both')
head(TAone.drl.analysis)

SCBIT-YYLab/DRAP documentation built on April 7, 2020, 2:03 a.m.