bootstrap_gene_finder: Function that perform a boostrap process from one cluster...

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

Description

Function that perform a boostrap process from one cluster over a set of other clusters applying at the end outlier analysis with dbscan.

Usage

bootstrap_gene_finder(
  cluster_number,
  seurat_object,
  LFC.lim = 0.2,
  use_limit = FALSE,
  maximo_genes = 20,
  bootstrap.number = 100,
  bootstrap.sample_size = NULL,
  min.p.adj_value = 0,
  ...
)

Arguments

cluster_number	Cluster number that the function has to process (TODO create a generalization for dataset with cluster with different names)
seurat_object	Seural object for single cells that enable us to apply the function FindMarkers
LFC.lim	a threshold of log fold change when selecting genes as input to perform Wilcoxon's test.
use_limit	TRUE/FALSE. If the process selects just a fixed number of genes.
maximo_genes	Maximum number of genes that have to be selected.
bootstrap.number	How many boostraping loops the algorithm is going to execute
min.p.adj_value	Value that should be greater or equal to zero. Normally it is 0.05

Value

List with the marker genes

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