curvep.RdThe relationship between concentration and response has to be 1 to 1.
The function is the backbone of run_rcurvep() and combi_run_rcurvep().
curvep( Conc, Resp, Mask = NULL, TRSH = 15, RNGE = -100, MXDV = 5, CARR = 0, BSFT = 3, USHP = 4, TrustHi = FALSE, StrictImp = TRUE, DUMV = -999, TLOG = -24, ... )
| Conc | Array of concentrations, e.g., in Molar units, can be log-transformed, in which case internal log-transformation is skipped. |
|---|---|
| Resp | Array of responses at corresponding concentrations, e.g., raw measurements or normalized to controls. |
| Mask | array of 1/0 flags indicating invalidated measurements (default = NULL). |
| TRSH | Base(zero-)line threshold (default = 15). |
| RNGE | Target range of responses (default = -100). |
| MXDV | Maximum allowed deviation from monotonicity (default = 5). |
| CARR | Carryover detection threshold (default = 0, analysis skipped if set to 0) |
| BSFT | For baseline shift issue, min.#points to detect baseline shift (default = 3, analysis skipped if set to 0). |
| USHP | For u-shape curves, min.#points to avoid flattening (default = 4, analysis skipped if set to 0). |
| TrustHi | For equal sets of corrections, trusts those retaining measurements at high concentrations (default = FALSE). |
| StrictImp | It prevents extrapolating over concentration-range boundaries; used for POD, ECxx etc (default = TRUE). |
| DUMV | A dummy value, default = -999. |
| TLOG | A scaling factor for calculating the wAUC, default = -24. |
| ... | allow other parameters to pass |
A list with corrected concentration-response measurements and several calculated curve metrics.
resp: corrected responses
corr: flags for corrections
ECxx: effective concentration values at various thresholds
Cxx: concentrations for various absolute response levels
Emax: maximum effective concentration, slope of the mid-curve (b/w EC25 and EC75)
wConc: response-weighted concentration
wResp: concentration-weighed response
POD: point-of-departure (first concentration with response >TRSH)
AUC: area-under-curve (in units of log-concentration X response)
wAUC: AUC weighted by concentration range and POD / TLOG (-24)
wAUC_pre: AUC weighted by concentration range and POD
nCorrected: number of points corrected (basically, sum of flags in corr)
Comments: warning and notes about the dose-response curve
Settings: input parameters for this run
Sedykh A, Zhu H, Tang H, Zhang L, Richard A, Rusyn I, Tropsha A (2011-March).
“Use of in vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in vivo toxicity.”
Environmental health perspectives, 119, 364--370.
doi: 10.1289/ehp.1002476
, http://europepmc.org/articles/PMC3060000.
Sedykh A (2016).
“CurveP Method for Rendering High-Throughput Screening Dose-Response Data into Digital Fingerprints.”
Methods in molecular biology (Clifton, N.J.), 1473, 135--141.
doi: 10.1007/978-1-4939-6346-1_14
.
#> $resp #> [1] 0 0 0 -15 -30 #> #> $corr #> [1] 0 0 0 0 0 #> #> $ECxx #> [1] -5.98 -5.90 -5.80 -5.60 -5.50 -5.00 -4.50 -4.40 -4.20 -4.10 -4.02 -4.00 #> #> $Cxx #> [1] -5.933333 -5.666667 -5.333333 -4.666667 -4.333333 -999.000000 #> [7] -999.000000 -999.000000 -999.000000 -999.000000 -999.000000 -999.000000 #> #> $xx #> [1] 1 5 10 20 25 50 75 80 90 95 99 100 #> #> $Emax #> [1] -30 #> #> $slope #> [1] -15 #> #> $wConc #> [1] -4.333333 #> #> $wResp #> [1] -6.5 #> #> $EC50 #> [1] -5 #> #> $C50 #> [1] -999 #> #> $POD #> [1] -5 #> #> $AUC #> [1] -30 #> #> $wAUC #> [1] -1.263158 #> #> $wAUC_prev #> [1] -37.5 #> #> $nCorrected #> [1] 0 #> #> $Comments #> [1] "OK" #> #> $Settings #> $Settings$TRSH #> [1] 15 #> #> $Settings$RNGE #> [1] -100 #> #> $Settings$MXDV #> [1] 5 #> #> $Settings$CARR #> [1] 0 #> #> $Settings$BSFT #> [1] 3 #> #> $Settings$USHP #> [1] 4 #> #> $Settings$TrustHi #> [1] FALSE #> #> $Settings$StrictImp #> [1] TRUE #> #> $Settings$DUMV #> [1] -999 #> #> $Settings$TLOG #> [1] -24 #> #>