annotate_clusters functionally annotates the identified clusters

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.

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')
#> 
#> Registered S3 method overwritten by 'enrichplot':
#>   method               from
#>   fortify.enrichResult DOSE
#> Loading required package: org.Hs.eg.db
#> Loading required package: AnnotationDbi
#> 
#> 'select()' returned 1:1 mapping between keys and columns
#> Warning: 8% of input gene IDs are fail to map...
#> Original gene number in geneList
#> 50
#> Number of genes successfully converted
#> 46
clusterProfiler::dotplot(enrichment_test, showCategory=15)