run_anabel {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
)

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)

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.

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)

See Also

convert_toMolar

Examples

# 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"
)