View source: R/perform.GO.enrichment.R
perform.GO.enrichment | R Documentation |
Performs gene ontology enrichment for individual cluster differential expression results.
perform.GO.enrichment( result, whichOnto = "BP", feasibleGenes = NULL, mapping = "org.Hs.eg.db", ID = "symbol", nodeSize = 5, algorithm = "classic", statistic = "ks", rank.cutoff = 0.001, gene.col = "gene", pval.col = "p_val", cluster.col = "cluster", n.top.pathways = 10 )
result |
A database containing the differential expression results |
whichOnto |
Character. specifying one of the three GO ontologies, namely: "BP", "MF", "CC". Default = 'BP' |
feasibleGenes |
Character vector. vector containing a subset of gene identifiers. Only these genes will be used to annotate GO terms. Default value is NULL which means that there are no genes filtered. |
mapping |
Character. The name of the Bioconductor package containing the gene mappings for a specific organism. For example: mapping = "org.Hs.eg.db". |
ID |
Character. Specify the gene identifier to use. Currently only the following identifiers can be used: c("entrez", "genbank", "alias", "ensembl", "symbol", "genename", "unigene") |
nodeSize |
Numerical. Minimum number of genes required to consider a GO term. Default = 5 |
algorithm |
Character. Which algorithm to use when testing for significant GO terms, options: 'classic', 'elim', 'weight', 'weight01', 'lea', 'parentchild'. Default = 'classic' |
statistic |
Character. Which statistic to use when testing for significant GO terms, options: 'fisher', 'ks', 't', 'globaltest', 'sum', 'ks.ties'. Default = 'ks' |
rank.cutoff |
Numerical. Which cut off to apply for pathway significance, this value will change according to the statistic applied. Default = 0.001 |
gene.col |
Character. Which column name within differential expression results contains the genes. Default = 'gene.col' |
pval.col |
Character. Which column name within differential expression results contains the p values. Default = 'p_val' |
cluster.col |
Character. Which column name within differential expression results contains the cluster assignments. Default = 'cluster' |
n.top.pathways |
Numerical. How many top pathways per group should be retained. Default = 10 |
A dataframe containing the top enriched pathways for each cluster
SCT_DE <- perform.seurat.diffexp.all(object = object, assay = 'SCT', test = 'MAST', identity = object@sample_metadata$celltype, latent.vars = 'original.project') SCT_DE_GO <- perform.GO.enrichment(result = SCT_DE) plot.GO.output(result = SCT_DE_GO) + ggplot2::ggtitle(label = 'SCT')
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