findMarkerGenes: Identify marker genes for each cluster.

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Identify marker genes for each cluster.

Description

Identify marker genes for each cluster.

Usage

findMarkerGenes(
  object,
  cluster.type = c("louvain", "walktrap", "kmeans", "merged_walktrap", "merged_louvain",
    "merged_kmeans"),
  min.log2FC = 0.5,
  min.expFraction = 0.3,
  limit.top.genes = 500,
  use.sampling.cells = FALSE,
  use.fraction.of.cells = 0.2,
  n.seed = 1
)

Arguments

object	The SingCellaR object.
cluster.type	The type of clustering method.
min.log2FC	The minimum cutoff of the log2FC. Default 0.5
min.expFraction	The minimum expressing cells fraction. Default 0.3
limit.top.genes	The limited number of differential genes to be shown. Default 500
use.sampling.cells	is logical. If TRUE, the downsample cells will be processed.
use.fraction.of.cells	The fraction of downsample. Default 0.2
n.seed	The number of set seed.

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.