runSDAv1_2D: Run SDA V1.1 in 2D i.e., matrix form

In eisascience/scCustFx: single-cell custom fxs Package

Run SDA V1.1 in 2D i.e., matrix form

Description

Executes the SDA algorithm on preprocessed and normalized single-cell gene expression data, allowing for dimensionality reduction and analysis. This function is designed to work with the specified version of SDA, taking in several parameters to customize the analysis process, including the number of components, iteration settings, and parallel processing options.

Usage

runSDAv1_2D(
  path.sda,
  resultsDir,
  rawDataFile,
  numComps = 30,
  max_iter = 100,
  save_freq = 20,
  set_seed = 1234,
  n_cells,
  nThreads = 6,
  num_blocks = 6
)

Arguments

path.sda	A character string specifying the path to the SDA software executable.
resultsDir	A character string specifying the directory where the SDA results will be saved.
rawDataFile	A character string specifying the path to the preprocessed and normalized gene expression data file to be analyzed.
numComps	Integer, the number of components to be used in the analysis, default is 30.
max_iter	Integer, the maximum number of iterations for the SDA algorithm, default is 100.
save_freq	Integer, frequency of saving interim results, default is 20 iterations.
set_seed	Integer, the seed for random number generation to ensure reproducibility, default is 1234.
n_cells	Integer, the number of cells in the dataset to be analyzed.
nThreads	Integer, the number of threads for parallel processing, default is 6. If greater than 1, eigen decomposition will be done in parallel.
num_blocks	Integer, the number of blocks to divide the dataset into for parallel processing, default is 6.

Value

Invisible NULL. The function is called for its side effects, including the execution of the SDA analysis and saving of results to the specified directory.

eisascience/scCustFx documentation built on June 2, 2025, 3:59 a.m.