identifyGSEAPrerankedGenes_in_a_cluster_vs_the_rest_of_clusters: Identify GSEA's preranked genes for a selected cluster vs the...

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

Identify GSEA's preranked genes for a selected cluster vs the rest of clusters

Description

Identify GSEA's preranked genes for a selected cluster vs the rest of clusters

Usage

identifyGSEAPrerankedGenes_in_a_cluster_vs_the_rest_of_clusters(
  object,
  cluster.id = "",
  cluster.type = c("louvain", "kmeans", "merged_walktrap", "merged_louvain",
    "merged_kmeans"),
  fishers_exact_test = 0.1,
  min.expFraction = 0.01,
  min.log2FC = 0.1,
  write.to.file = ""
)

Arguments

object	The SingCellaR object.
cluster.id	The specified cluster id (e.g. 'cluster1')
cluster.type	The type of clustering method.
fishers_exact_test	The fisher's exact test cutoff p-value. Default 0.1
min.expFraction	The minimum fraction of expressing cell frequency cutoff. Default 0.01
min.log2FC	The minimum log2FC cutoff. Default 0.1
write.to.file	The output file name.

Value

a dataframe of preranked genes.

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