Description Usage Arguments Details Value See Also Examples
DRE object represents a dose-response experiment. This function creates a new DRE object from one or more Compound objects
1 2 3 4 |
.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 |
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:
fraction[i] = sqrt(min.dose[i]*max.dose[i]) / sum(sqrt(min.dose[1:n]*max.dose[1:n]))
min.dose = 1/sum(fraction[1:n]/min.dose[1:n])
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
:
"exp" series is exponential, e.g. 1,2,4,8,16
"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.
DRE object
DRE, Compound
1 2 3 4 5 6 | 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")
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