Optimise registration parameters with Simulated Annealing

Usage

optimise_registration_params(
  input_df,
  genes = NULL,
  stretches_bound = NA,
  shifts_bound = NA,
  initial_rescale = FALSE,
  do_rescale = TRUE,
  min_num_overlapping_points = 4,
  maintain_min_num_overlapping_points = FALSE,
  accession_data_to_transform,
  accession_data_ref,
  start_timepoint = c("reference", "transform", "zero"),
  expression_value_threshold = 5,
  is_data_normalised = FALSE,
  num_iterations = 60
)

Arguments

input_df: Input data frame containing all replicates of gene expression in each genotype at each time point.
genes: List of genes to optimise.
stretches_bound: Optional candidate registration stretch factors define search space, otherwise automatic.
shifts_bound: Optional candidate registration shift values to define search space, otherwise automatic.
initial_rescale: Scaling gene expression prior to registration if TRUE.
do_rescale: Scaling gene expression using only overlapping time points points during registration.
min_num_overlapping_points: Number of minimum overlapping time points. Shifts will be only considered if it leaves at least these many overlapping points after applying the registration function.
maintain_min_num_overlapping_points: Whether to automatically calculate extreme (minimum and maximum) values of shifts to maintain specified min_num_overlapping_points condition. By default, FALSE.
accession_data_to_transform: Accession name of data which will be transformed.
accession_data_ref: Accession name of reference data.
start_timepoint: Time points to be added in both reference data and data to transform after shifting and stretching. Can be either "reference" (the default), "transform", or "zero".
expression_value_threshold: Expression value threshold. Remove expressions if maximum is less than the threshold. If NULL keep all data.
is_data_normalised: TRUE if dataset has been normalised prior to registration process.
num_iterations: Maximum number of iterations of the algorithm. Default is 100.

Value

List of optimum registration parameters, optimum_params_df, and other candidate registration parameters, candidate_params_df for all genes.