initialize-DRE-method: Initialise a DRE object

Description Usage Arguments Details Value See Also Examples

Description

DRE object represents a dose-response experiment. This function creates a new DRE object from one or more Compound objects

Usage

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## S4 method for signature 'DRE'
initialize(.Object, compound.name, name = NULL, compound,
  fraction = NULL, dose = NULL, min.dose = NULL, max.dose = NULL,
  num.doses = 5, dose.series.type = "exp", dilution.factor.decimals = 2)

Arguments

.Object

object of class DRE

compound.name

names of compounds that are included in the dre object, character

name

optional name of the dose-response experiment, character

compound

a list of Compound objects

fraction

optional vector of compound fractions, numeric, should add up to 1

dose

optional vector of doses. In case of mixtures, these are the doses of an entire mixture.

min.dose

optional minimal dose, numeric.

max.dose

optional maximal dose, numeric.

num.doses

number of different doses in the dose-response experiment

dose.series.type

the type of dose series. Supported values are "exp" and "linear". See the Details.

dilution.factor.decimals

integer number of decimal points in the dilution factor

Details

Generally, a dose-response experiment is conducted on a mixture of compounds. Suppose each compound is referred to by an index i and there are n compounds.

If parameters fraction and dose are both supplied by the caller, the following must be true: dose[j] = SUM(fraction[i]*dose[ij]) where dose[j] is the j'th dose of the mixture and dose[ij] is the j'th dose of an individual compound

If not supplied by the caller, parameters fraction, min.dose and max.dose are computed as follows:

  1. fraction[i] = sqrt(min.dose[i]*max.dose[i]) / sum(sqrt(min.dose[1:n]*max.dose[1:n]))

  2. min.dose = 1/sum(fraction[1:n]/min.dose[1:n])

  3. max.dose = 1/sum(fraction[1:n]/max.dose[1:n])

Unless the dose parameter is supplied by the caller, the doses are calculated as a series of num.doses values from min.dose to max.dose. The type of the series is determined by dose.series.type:

  1. "exp" series is exponential, e.g. 1,2,4,8,16

  2. "linear" series is linear, e.g. 1,2,3,4,5

In exponential dose series, the minimal dose will not be exactly the same as min.dose supplied by the caller. The initialize method will round the dilution factor to the number of decimals specified by parameter dilution.factor.decimals. Resulting minimal dose should be reasonably close to the supplied min.dose parameter, but won't equal it exactly.

Value

DRE object

See Also

DRE, Compound

Examples

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data(sim15_screen3)
compound(sim15_screen3,"Cpd1")
new("DRE", compound.name="Cpd1", compound=list(compound(sim15_screen3,"Cpd1")), 
    num.doses=5, dose.series.type="exp")
new("DRE", compound.name="Cpd1", compound=list(compound(sim15_screen3,"Cpd1")), 
    num.doses=5, dose.series.type="linear")

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