dot-computeZIPdelta: Vector-based version of computeZIPdelta

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

Vector-based version of computeZIPdelta

Description

Following the calculation of ZIP delta score as in Appendix A3. See reference for details.

Usage

.computeZIPdelta(
  treatment1id,
  treatment2id,
  treatment1dose,
  treatment2dose,
  sampleid,
  HS_1,
  HS_2,
  EC50_1,
  EC50_2,
  E_inf_1,
  E_inf_2,
  combo_viability,
  ZIP = NULL,
  residual = "logcosh",
  nthread = 1L,
  show_Rsqr = FALSE
)

Arguments

treatment1id	character a vector of identifiers for treatment 1
treatment2id	character a vector of identifiers for treatment 2
treatment1dose	numeric a vector of concentrations for treatment 1
treatment2dose	numeric a vector of concentrations for treatment 2
sampleid	character Cell-line ID of a drug combination screening experiment.
HS_1	numeric Hill coefficient of treatment 1
HS_2	numeric Hill coefficient of treatment 2
EC50_1	numeric relative EC50 of treatment 1.
EC50_2	numeric relative EC50 of treatment 2.
E_inf_1	numeric viability produced by the maximum attainable effect of treatment 1.
E_inf_2	numeric viability produced by the maximum attainable effect of treatment 2.
combo_viability	numeric observed viability of the two treatments combined.
ZIP	numeric pre-computed ZIP reference values. If not provided, it will be computed during delta score calculation.
residual	character Method used to minimise residual in fitting curves. 3 methods available: c("logcosh", "normal", "Cauchy"). The default method is logcosh. It minimises the logarithmic hyperbolic cosine loss of the residuals and provides the fastest estimation among the three methods, with fitting quality in between normal and Cauchy; recommanded when fitting large-scale datasets. The other two methods minimise residuals by considering the truncated probability distribution (as in their names) for the residual. Cauchy provides the best fitting quality but also takes the longest to run.
nthread	integer Number of cores used to perform computation. Default 1.
show_Rsqr	logical Whether to show the 2-way curve fitting quality in the result. Default FALSE.

Value

numeric delta scores of every dose combinations for any given treatment combinations.

References

Yadav, B., Wennerberg, K., Aittokallio, T., & Tang, J. (2015). Searching for Drug Synergy in Complex Dose–Response Landscapes Using an Interaction Potency Model. Computational and Structural Biotechnology Journal, 13, 504–513. https://doi.org/10.1016/j.csbj.2015.09.001

Examples

## Not run: 
## ZIP is optional. Will be recomputed if not provided.
combo_profiles <- CoreGx::buildComboProfiles(
     tre, 
     c("HS", "EC50", "E_inf", "ZIP", "combo_viability"))
combo_profiles[,
        .computeZIPdelta(
            treatment1id = treatment1id,
            treatment2id = treatment2id,
            treatment1dose = treatment1dose,
            treatment2dose = treatment2dose,
            sampleid = sampleid,
            HS_1 = HS_1, HS_2 = HS_2,
            EC50_1 = EC50_1, EC50_2 = EC50_2,
            E_inf_1 = E_inf_1, E_inf_2 = E_inf_2,
            combo_viability = combo_viability,
            ZIP = ZIP,
            nthread = 4,
            show_Rsqr = TRUE
        )
    ] -> delta_scores

## End(Not run)

bhklab/PharmacoGx documentation built on April 18, 2024, 3:13 a.m.