annotate_clusters {scGPS}R Documentation

annotate_clusters functionally annotates the identified clusters

Description

often we need to label clusters with unique biological characters. One of the common approach to annotate a cluster is to perform functional enrichment analysis. The annotate implements ReactomePA and clusterProfiler for this analysis type in R. The function require installation of several databases as described below.

Usage

annotate_clusters(
  DEgeneList,
  pvalueCutoff = 0.05,
  gene_symbol = TRUE,
  species = "human"
)

Arguments

DEgeneList

is a vector of gene symbols, convertable to ENTREZID

pvalueCutoff

is a numeric of the cutoff p value

gene_symbol

logical of whether the geneList is a gene symbol

species

is the selection of 'human' or 'mouse', default to 'human' genes

Value

write enrichment test output to a file and an enrichment test object for plotting

Examples

genes <-training_gene_sample
genes <-genes$Merged_unique[seq_len(50)]
enrichment_test <- annotate_clusters(genes, pvalueCutoff=0.05, 
    gene_symbol=TRUE, species = 'human')
clusterProfiler::dotplot(enrichment_test, showCategory=15)


[Package scGPS version 1.6.0 Index]