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 1.8.0 Index]