iteration_over_clusters_parallelized_wilcox: Marker gene selection with parallelization using wilcox...

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

Description

Marker gene selection with parallelization using wilcox method from the Seurat library

Usage

iteration_over_clusters_parallelized_wilcox_outlier(
  sc.eset,
  ct.group,
  core_number = NULL,
  LFC.lim = 0.2,
  minimun_number_markers = 20,
  minimum_genes_pipeline = TRUE,
  add_zero_p_val_adj = TRUE,
  minimum_p_val_adj = 0,
  maximo_genes = 20,
  ...
)

Arguments

sc.eset	ExpressionSet object for single cells
ct.group	List of clusters that will be analyzed
core_number	Number of cores that will be used for the process.
LFC.lim	a threshold of log fold change when selecting genes as input to perform Wilcoxon's test.
minimun_number_markers	If the variable minimum_genes_pipeline is active and also if in the first step with the wilcox text there are at least this genes, the process is not going to use outlier detection with dbscan
minimum_genes_pipeline	TRUE/FALSE. Parameter that enable the minimum gene process using outlier detection. If is FALSE the process is not going to run and the genes would be the ones found for wilcox test
add_zero_p_val_adj	TRUE/FALSE. If after the dbscan we want to add the genes that were found with the normal wilcox detection using the threshold (normally 0 or 0.05)
minimum_p_val_adj	p-value-adjusted for the wilcox process. Could be zero or 0.05
maximo_genes	If we want to limitate the maximum number of marker genes at the end of the process.

Value

List with the marker genes for all selected clusters

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