concRespCore: Concentration Response Core
In tcplfit2: Concentration-Response Modeling of HTS or Transcriptomics Data

concRespCore

R Documentation

Concentration Response Core

Description

Core of concentration response curve fitting for pvalue based cutoff. This function calls tcplfit2_core to get curve fits, and then tcplhit2_core to perform the hitcalling.

Usage

concRespCore(
  row,
  fitmodels = c("cnst", "hill", "gnls", "poly1", "poly2", "pow", "exp2", "exp3", "exp4",
    "exp5"),
  conthits = TRUE,
  aicc = FALSE,
  force.fit = FALSE,
  bidirectional = TRUE,
  verbose = FALSE,
  do.plot = FALSE,
  return.details = FALSE,
  bmr_scale = 1.349,
  bmd_low_bnd = NULL,
  bmd_up_bnd = NULL
)

Arguments

`row`	A named list that must include: conc - list of concentrations (not in log units) resp - list of corresponding responses bmed - median of noise estimate. cutoff - noise cutoff onesd - 1 standard deviation of the noise (for bmd calculation) Other elements (usually identifiers, like casrn) of row will be attached to the final output.
`fitmodels`	Vector of model names to use.
`conthits`	conthits = TRUE uses continuous hitcalls, otherwise they're discrete.
`aicc`	aicc = TRUE uses corrected AIC to choose winning method; otherwise regular AIC.
`force.fit`	If TRUE force the fitting to proceed even if there are no points outside of the bounds (default FALSE)
`bidirectional`	If TRUE allow fitting to happen in both directions (default TRUE)
`verbose`	If TRUE, write extra output from tcplfit2_core (default FALSE)
`do.plot`	If TRUE, create a plot in the tcplfit2_core function (default FALSE)
`return.details`	If TRUE, return the hitcalling details and the summary, if FALSE (default), just return the summary
`bmr_scale`	- bmr scaling factor (for bmd calculation) default = 1.349
`bmd_low_bnd`	Multiplier for bmd lower bound. A value of .1 would require the bmd to be no lower than 1/10th of the lowest concentration tested.
`bmd_up_bnd`	Multiplier for the bmd upper bound. A value of 10 would require the bmd to be no lower than 10 times the highest concentration tested.

Value

A list of two elements. The first (summary) is the output from tcplhit2_core. The second, params is the output from tcplfit2_core a dataframe of one row containing

Examples

conc <- list(.03, .1, .3, 1, 3, 10, 30, 100)
resp <- list(0, .2, .1, .4, .7, .9, .6, 1.2)
row <- list(conc = conc,
            resp = resp,
            bmed = 0,
            cutoff = 1,
            onesd = .5,
            name = "some chemical",
            assay = "some assay")
concRespCore(row, conthits = TRUE)
concRespCore(row, aicc = TRUE)

tcplfit2 documentation built on Oct. 11, 2023, 1:07 a.m.