Sanity Check for Input Data and Parameters

This function performs a series of checks and initial setups for input data, metadata, and parameters, ensuring everything is correctly formatted for downstream analysis.

SanityChecK(
  x,
  niter = 1000,
  K = NULL,
  meta.info,
  group.name,
  formula.str,
  verbose = TRUE,
  log = TRUE
)

Arguments

x: A matrix-like object or a SummarizedExperiment containing the data to be analyzed.
niter: Integer. Number of bootstrap samples or resampling iterations. Default is 1000.
K: Integer. Top list size. If NULL, it will be set to a quarter of the number of rows in the data matrix. Default is NULL.
meta.info: Data frame. Metadata associated with the samples (columns of data.exp). If data.exp is a SummarizedExperiment, meta.info can be a vector of colData column names to use.
group.name: Character. Column name in meta.info that defines the groups or conditions for comparison.
formula.str: Optional character string representing the formula for the model.
verbose: Logical, indicating whether to display messages during the function's execution. Default is TRUE.
log: Logical, indicating whether the data is already log-transformed. Default is TRUE.

Value

A list containing:

meta.info: Processed metadata.
data: Processed data matrix.
groups: Numeric or factor vector indicating group assignments.
K: Top list size to be used in the analysis.

Details

This function checks whether the input data and metadata are in the correct format, processes metadata from a SummarizedExperiment object if provided, and ensures that group information is correctly specified. If no top list size (K) is provided, it defaults to a quarter of the number of rows in the data.