run_anabel: Analysis for 1:1 Biomolecular Interactions

Description

Analysis for 1:1 biomolecular interactions, using one of single-curve analysis (SCA), single-cycle kinetics (SCK) or multi-cycle kinetics (MCK)

Usage

run_anabel(
  input = NA,
  samples_names_file = NULL,
  tstart = NA,
  tend = NA,
  tass = NA,
  tdiss = NA,
  conc = NA,
  drift = FALSE,
  decay = FALSE,
  quiet = TRUE,
  method = "SCA",
  outdir = NA,
  generate_output = "none",
  generate_Report = FALSE,
  generate_Plots = FALSE,
  generate_Tables = FALSE,
  save_tables_as = "xlsx",
  debug_mode = FALSE
)

Value

default returned value is a list of two data frames, the kinetics table and the fit value of each time point (fit_raw). If dev_mode was set to TRUE a third data frame will be returned containing the initial value of the parameters and the fitting function.

Arguments

input: Data.frame, an excel, or a csv file (full path) - required
samples_names_file: An optional data.frame, an excel, or a csv file (full path) containing the samples names. If provided, it must have two columns, Name and ID. ID: names of columns in the input file; Name: sample's names.
tstart: Numeric value of time's starting point (default: minimum time point in the input)
tend: Numeric value of time's ending point (default: maximum time point in the input)
tass: Numeric value of association time - required
tdiss: Numeric value of dissociation time - required
conc: Numeric value, the used concentration of the analyte; should be in molar (see convert_toMolar) - required
drift: Boolean value, to apply drift correction (default: FALSE)
decay: Boolean value, to apply surface decay correction (default: FALSE)
quiet: Boolean value, to suppress notifications, messages and warnings (default: TRUE)
method: a character string indicating which fitting method to be used. One of "SCA", "SCK", or "MCK", case insensitive (default: SCA).
outdir: Path and name of the output directory in which the results will be saved (default: NA)
generate_output: a character string indicating what kind of output will be generated. One of "none", "all", or "customized", case insensitive (default: none). If "all" or "customized" were given, outdir is required. If "customized" was given, at least one of generate_Plots, generate_Tables, or/and generate_Report must be set to TRUE
generate_Report: Boolean value, should anabel generate a summary report of the experiment? (default: FALSE)
generate_Plots: Boolean value, should anabel generate plots? (default: FALSE). generate_output must be set to "customized"
generate_Tables: Boolean value, should anabel generate tables? (default: FALSE)
save_tables_as: a character string indicating data format to save the tables with; could be "xlsx", "csv", "txt" or "rds", case insensitive, (default: xlsx)
debug_mode: Boolean value, anabel will return additional fitting details for each curve and the estimated response (default: FALSE)

References

Determination of rate and equilibrium binding constants for macromolecular interactions by surface plasmon resonance. D J O'Shannessy, M Brigham-Burke, K K Soneson, P Hensley, I Brooks Analytical biochemistry 212, 457-468 (1993)

Analyzing a kinetic titration series using affinity biosensors. Robert Karlsson, Phinikoula S Katsamba, Helena Nordin, Ewa Pol, David G Myszka Analytical Biochemistry 349, 136–147 (2006)

Anabel: an online tool for the real-time kinetic analysis of binding events. Stefan D Krämer, Johannes Wöhrle , Christin Rath, Günter Roth Bioinformatics and Biology Insights 13, 1-10 (2019)

Examples

Run this code

# \donttest{
# To analyse data using MCK method:
run_anabel(
  input = MCK_dataset, tstart = 1, tass = 21, tdiss = 140,
  conc = c(3.9E-9, 1.6E-8, 6.2E-8, 2.5E-7, 1.0e-6), method = "MCK"
)
# }