identifyDifferentialGenes_in_a_cluster_vs_the_rest_of_clusters: Identify differentially expressed genes between a selected...

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

Identify differentially expressed genes between a selected cluster vs the rest of clusters

Description

Identify differentially expressed genes between a selected cluster vs the rest of clusters

Usage

identifyDifferentialGenes_in_a_cluster_vs_the_rest_of_clusters(
  object,
  cluster.id = "",
  method = c("wilcoxon"),
  cluster.type = c("louvain", "walktrap", "kmeans", "merged_walktrap", "merged_louvain",
    "merged_kmeans"),
  min.log2FC = 0.25,
  min.expFraction = 0.3,
  write.to.file = ""
)

Arguments

object	The SingCellaR object.
cluster.type	The type of clustering method.
min.log2FC	The minimum log2FC cutoff. Default 0.25
min.expFraction	The minimum fraction of expressing cell frequency cutoff. Default 0.3
write.to.file	The output file name.
cluster_id	The specified cluster ID (e.g. cluster1)

Value

a dataframe of differentially expressed genes.

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