Identify_Markers: Identify markers of each cluster

In CACIMAR: Cross-Species Analysis of Cell Identities, Markers and Regulations

Identify markers of each cluster

Description

This function first identify marker genes in each cluster with Roc threshold > RocThr. Then, based on marker genes identified above, this function calculates the difference and power of marker genes in each cluster, and marker genes with Difference threshold > DiffThr will be retained. Next, gene with the largest power in which cluster will be the marker gene in this cluster. Eventually, make fisher test for power of each cluster, cluster with p.value < 0.05 will be retained as the final cluster for marker gene

Usage

Identify_Markers(
  Seurat_object,
  PowerCutoff = 0.4,
  DifferenceCutoff = 0,
  PvalueCutoff = 0.05
)

Arguments

Seurat_object	Seurat object, should contain cluster information
PowerCutoff	numeric, indicating the cutoff of gene power to refine marker genes
DifferenceCutoff	numeric, indicating the cutoff of difference in marker genes between clusters to refine marker genes
PvalueCutoff	numeric, indicating the p.value cutoff of chi-square test to refine marker genes

Value

Data frame of conserved markers

Examples

data("pbmc_small")
all.markers <- Identify_Markers(pbmc_small)

CACIMAR documentation built on May 18, 2022, 9:07 a.m.