iteration_over_clusters_parallelized: Paralellization of the for procedure for QC process

In crhisto/SCDC: Bulk RNA-seq deconvolution by scRNA-seq with multi-reference datasets

Description

It contains some experiments but is not the final version. It is just saved for documentation purposes.

Usage

qc_iteration_parallelized(
  m.basis,
  xsc,
  sigma,
  N.sc,
  nu,
  epsilon,
  iter.max,
  core_number = NULL,
  ...
)

iteration_over_clusters_parallelized(
  ct.group,
  LFC.lim,
  sc.eset,
  top_genes,
  pseudocount.use,
  core_number = NULL,
  fix_number_genes = NULL,
  ...
)

Arguments

nu	a small constant to facilitate the calculation of variance
epsilon	a small constant number used for convergence criteria
iter.max	the maximum number of iteration in WNNLS
core_number	Number of cores that will be used for the process.
ct.group	List of clusters that will be analyzed
LFC.lim	a threshold of log fold change when selecting genes as input to perform Wilcoxon's test.
sc.eset	ExpressionSet object for single cells
top_genes	Number of top genes that we want to consider to check the maximum LFC for each cluster. This is just for informative purposes.
fix_number_genes	Maximum number of marker genes that has to be returned by cluster

Value

List with the marker genes for all selected clusters

crhisto/SCDC documentation built on Dec. 19, 2021, 6:19 p.m.