register: Register or synchronize different expression profiles

In greatR: Gene Registration from Expression and Time-Courses in R

Register or synchronize different expression profiles

Description

register() is a function to register expression profiles a user wishes to compare.

Usage

register(
  input,
  stretches = NA,
  shifts = NA,
  reference,
  query,
  scaling_method = c("scale", "normalise"),
  overlapping_percent = 0.5,
  optimise_registration_parameters = TRUE,
  optimisation_method = c("nm", "lbfgsb", "sa"),
  optimisation_config = NULL
)

Arguments

input	Input data frame containing all replicates of gene expression in each genotype at each time point.
stretches	Candidate registration stretch factors to apply to query data, only required if optimise_registration_parameters = FALSE.
shifts	Candidate registration shift values to apply to query data, only required if optimise_registration_parameters = FALSE.
reference	Accession name of reference data.
query	Accession name of query data.
scaling_method	Scaling method applied to data prior to registration process. Either scale (default), or normalise.
overlapping_percent	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.
optimise_registration_parameters	Whether to optimise registration parameters with Simulated Annealing. By default, TRUE.
optimisation_method	Optimisation method to use. Either "nm" for Nelder-Mead (default), "lbfgsb" for L-BFGS-B, or "sa" for Simulated Annealing.
optimisation_config	Optional list with arguments to override the default optimisation configuration.

Value

This function returns a list of data frames, containing:

data	a table containing the scaled input data and an additional timepoint_reg column after applying registration parameters to the query data.
model_comparison	a table comparing the optimal registration function for each gene (based on all_shifts_df scores) to model with no registration applied.

Examples

## Not run: 
# Load a data frame from the sample data
data_path <- system.file("extdata/brapa_arabidopsis_all_replicates.csv", package = "greatR")
all_data <- utils::read.csv(data_path)

# Running the registration
registration_results <- register(
  input = all_data,
  reference = "Ro18",
  query = "Col0"
)

## End(Not run)

greatR documentation built on July 26, 2023, 5:43 p.m.