getModelParamsDf: Get H0 and H1 model parameters

In nkurzaw/TPP2D: Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)

Get H0 and H1 model parameters

Description

Get H0 and H1 model parameters

Usage

getModelParamsDf(
  df,
  minObs = 20,
  optim_fun_h0 = .min_RSS_h0,
  optim_fun_h1 = .min_RSS_h1_slope_pEC50,
  optim_fun_h1_2 = NULL,
  gr_fun_h0 = NULL,
  gr_fun_h1 = NULL,
  gr_fun_h1_2 = NULL,
  slopEC50 = TRUE,
  maxit = 500,
  qualColName = "qupm"
)

Arguments

df	tidy data_frame retrieved after import of a 2D-TPP dataset, potential filtering and addition of a column "nObs" containing the number of observations per protein
minObs	numeric value of minimal number of observations that should be required per protein
optim_fun_h0	optimization function that should be used for fitting the H0 model
optim_fun_h1	optimization function that should be used for fitting the H1 model
optim_fun_h1_2	optional additional optimization function that will be run with paramters retrieved from optim_fun_h1 and should be used for fitting the H1 model with the trimmed sum model, default is NULL
gr_fun_h0	optional gradient function for optim_fun_h0, default is NULL
gr_fun_h1	optional gradient function for optim_fun_h1, default is NULL
gr_fun_h1_2	optional gradient function for optim_fun_h1_2, default is NULL
slopEC50	logical flag indicating whether the h1 model is fitted with a linear model describing the shift od the pEC50 over temperatures
maxit	maximal number of iterations the optimization should be given, default is set to 500
qualColName	name of column indicating quantification quality e.g. number of unique peptides used for quantification, default: "qupm"

Value

a data.frame with fitted null and alternative model parameters

Examples

data("simulated_cell_extract_df")
getModelParamsDf(simulated_cell_extract_df)

nkurzaw/TPP2D documentation built on May 9, 2023, 10:04 a.m.