transferTrueValues: Transfer "true" values of various parameters from one object...

In ybukhman/SynergyScreen: Analyze and simulate synergy screen data

Description

Transfer "true" values of various parameters from one object to another

Usage

transferTrueValues(from, to)

## S4 method for signature 'Compound,Compound'
transferTrueValues(from, to)

## S4 method for signature 'DRE,DRE'
transferTrueValues(from, to)

## S4 method for signature 'SynergyScreen,SynergyScreen'
transferTrueValues(from, to)

Arguments

from	object to transfer values from
to	object to transfer values to

Details

These methods are useful in multi-step simulations, when "ground truth" values, e.g. "true" values of IC50 and m parameters of dose-response curves, need to be transferred from one step to the next

Value

Object "to" with modified slots

## Stage 1: simulate individual compounds and their dose-response experiments # Load a set of compounds and initialize a SynergyScreen object cpds = readCompoundFile(system.file("extdata/15_cpds_simulation/compounds_1.csv", package="SynergyScreen")) screen1 = new("SynergyScreen",compound_list=cpds)

# Generate screen design, only testing single compounds at first screen1 = generateDesign(screen1,pairs=FALSE)

# Simulate compound growth curve characteristics and raw dose-response data set.seed(20141120) screen1 = simulate(screen1)

# Normalize screen data, adjusting for plate bias screen1 = normalize(screen1)

# Check ranges of dose-response experiments screen1 = checkRange(screen1)

## Stage 2: re-do dose-response experiments for which dose range checks failed, ## with corrected dose ranges # Load the new set of compounds, initialize a SynergyScreen object and generate a design cpds2 = readCompoundFile(system.file("extdata/15_cpds_simulation/compounds_2.csv", package="SynergyScreen")) screen2 = new("SynergyScreen",compound_list=cpds2) screen2 = generateDesign(screen2,pairs=FALSE)

#====================================================================================# ### Transfer previously simulated "true" IC50 and m values to compounds in screen2 ### screen2 = transferTrueValues(screen1,screen2) compound(screen1,"Cpd1") compound(screen2,"Cpd1") #====================================================================================##

# Simulate dose-response data again set.seed(20141121) screen2 = simulate(screen2) screen2 = normalize(screen2) screen2 = checkRange(screen2)

Methods (by class)

• from = Compound,to = Compound: Transfer "true" IC50 and m values between simulated Compound objects

• from = DRE,to = DRE: Transfer previously simulated "true" IC50 and m values from one DRE object to another

• from = SynergyScreen,to = SynergyScreen: Transfer previously simulated "true" IC50 and m values from one SynergyScreen object to another

See Also

Compound, DRE, SynergyScreen,

ybukhman/SynergyScreen documentation built on May 4, 2019, 2:31 p.m.