Perform the enrichment analysis (over-representation) on the genes

Usage

RunEnrichment(
  srt = NULL,
  group_by = NULL,
  test.use = "wilcox",
  DE_threshold = "avg_log2FC > 0 & p_val_adj < 0.05",
  geneID = NULL,
  geneID_groups = NULL,
  geneID_exclude = NULL,
  IDtype = "symbol",
  result_IDtype = "symbol",
  species = "Homo_sapiens",
  db = "GO_BP",
  db_update = FALSE,
  db_version = "latest",
  db_combine = FALSE,
  convert_species = TRUE,
  Ensembl_version = 103,
  mirror = NULL,
  TERM2GENE = NULL,
  TERM2NAME = NULL,
  minGSSize = 10,
  maxGSSize = 500,
  unlimited_db = c("Chromosome", "GeneType", "TF", "Enzyme", "CSPA"),
  GO_simplify = FALSE,
  GO_simplify_cutoff = "p.adjust < 0.05",
  simplify_method = "Wang",
  simplify_similarityCutoff = 0.7,
  BPPARAM = BiocParallel::bpparam(),
  seed = 11
)

Arguments

srt: A Seurat object containing the results of differential expression analysis (RunDEtest). If specified, the genes and groups will be extracted from the Seurat object automatically. If not specified, the geneID and geneID_groups arguments must be provided.
group_by: A character vector specifying the grouping variable in the Seurat object. This argument is only used if srt is specified.
test.use: A character vector specifying the test to be used in differential expression analysis. This argument is only used if srt is specified.
DE_threshold: A character vector specifying the filter condition for differential expression analysis. This argument is only used if srt is specified.
geneID: A character vector specifying the gene IDs.
geneID_groups: A factor vector specifying the group labels for each gene.
geneID_exclude: A character vector specifying the gene IDs to be excluded from the analysis.
IDtype: A character vector specifying the type of gene IDs in the srt object or geneID argument. This argument is used to convert the gene IDs to a different type if IDtype is different from result_IDtype.
result_IDtype: A character vector specifying the desired type of gene ID to be used in the output. This argument is used to convert the gene IDs from IDtype to result_IDtype.
species: A character vector specifying the species for which the analysis is performed.
db: A character vector specifying the name of the database to be used for enrichment analysis.
db_update: A logical value indicating whether the gene annotation databases should be forcefully updated. If set to FALSE, the function will attempt to load the cached databases instead. Default is FALSE.
db_version: A character vector specifying the version of the database to be used. This argument is ignored if db_update is TRUE. Default is "latest".
db_combine: A logical value indicating whether to combine multiple databases into one. If TRUE, all database specified by db will be combined as one named "Combined".
convert_species: A logical value indicating whether to use a species-converted database when the annotation is missing for the specified species. The default value is TRUE.
Ensembl_version: Ensembl database version. If NULL, use the current release version.
mirror: Specify an Ensembl mirror to connect to. The valid options here are 'www', 'uswest', 'useast', 'asia'.
TERM2GENE: A data frame specifying the gene-term mapping for a custom database. The first column should contain the term IDs, and the second column should contain the gene IDs.
TERM2NAME: A data frame specifying the term-name mapping for a custom database. The first column should contain the term IDs, and the second column should contain the corresponding term names.
minGSSize: A numeric value specifying the minimum size of a gene set to be considered in the enrichment analysis.
maxGSSize: A numeric value specifying the maximum size of a gene set to be considered in the enrichment analysis.
unlimited_db: A character vector specifying the names of databases that do not have size restrictions.
GO_simplify: A logical value indicating whether to simplify the GO terms. If TRUE, additional results with simplified GO terms will be returned.
GO_simplify_cutoff: A character vector specifying the filter condition for simplification of GO terms. This argument is only used if GO_simplify is TRUE.
simplify_method: A character vector specifying the method to be used for simplification of GO terms. This argument is only used if GO_simplify is TRUE.
simplify_similarityCutoff: A numeric value specifying the similarity cutoff for simplification of GO terms. This argument is only used if GO_simplify is TRUE.
BPPARAM: A BiocParallelParam object specifying the parallel back-end to be used for parallel computation. Defaults to BiocParallel::bpparam().
seed: The random seed for reproducibility. Defaults to 11.

Value

If input is a Seurat object, returns the modified Seurat object with the enrichment result stored in the tools slot.

If input is a geneID vector with or without geneID_groups, return the enrichment result directly.

Enrichment result is a list with the following component:

enrichment: A data.frame containing all enrichment results.
results: A list of enrichResult objects from the DOSE package.
geneMap: A data.frame containing the ID mapping table for input gene IDs.
input: A data.frame containing the input gene IDs and gene ID groups.
DE_threshold: A specific threshold for differential expression analysis (only returned if input is a Seurat object).

Examples

data("pancreas_sub")
pancreas_sub <- RunDEtest(pancreas_sub, group_by = "CellType")
#> Warning: Data in the 'data' slot is raw counts. Perform NormalizeData(LogNormalize) on the data.
#> [2023-11-21 07:37:53.015774] Start DEtest
#> Workers: 2
#> Find all markers(wilcox) among 5 groups...
#> 
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#> 
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#> 
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#> 
#> [2023-11-21 07:38:03.458278] DEtest done
#> Elapsed time:10.44 secs
pancreas_sub <- RunEnrichment(
  srt = pancreas_sub, group_by = "CellType", DE_threshold = "p_val_adj < 0.05",
  db = "GO_BP", species = "Mus_musculus"
)
#> [2023-11-21 07:38:03.46236] Start Enrichment
#> Workers: 2
#> Species: Mus_musculus
#> Loading cached db: GO_BP version:3.17.0 nterm:16027 created:2023-11-21 07:14:20.545084
#> Convert ID types for the database: GO_BP
#> Connect to the Ensembl archives...
#> Using the 103 version of biomart...
#> Connecting to the biomart...
#> Searching the dataset mmusculus ...
#> Connecting to the dataset mmusculus_gene_ensembl ...
#> Converting the geneIDs...
#> Error in collect(., Inf): Failed to collect lazy table.
#> Caused by error in `db_collect()`:
#> ! Arguments in `...` must be used.
#> ✖ Problematic argument:
#> • ..1 = Inf
#> ℹ Did you misspell an argument name?
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", plot_type = "comparison")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType",     plot_type = "comparison"): No enrichment result found. You may perform RunEnrichment first.

pancreas_sub <- RunEnrichment(
  srt = pancreas_sub, group_by = "CellType", DE_threshold = "p_val_adj < 0.05",
  db = c("MSigDB", "MSigDB_MH"), species = "Mus_musculus"
)
#> [2023-11-21 07:38:07.637929] Start Enrichment
#> Workers: 2
#> Species: Mus_musculus
#> Preparing database: MSigDB
#> Convert ID types for the database: MSigDB
#> Connect to the Ensembl archives...
#> Using the 103 version of biomart...
#> Connecting to the biomart...
#> Searching the dataset mmusculus ...
#> Connecting to the dataset mmusculus_gene_ensembl ...
#> Converting the geneIDs...
#> Error in collect(., Inf): Failed to collect lazy table.
#> Caused by error in `db_collect()`:
#> ! Arguments in `...` must be used.
#> ✖ Problematic argument:
#> • ..1 = Inf
#> ℹ Did you misspell an argument name?
EnrichmentPlot(pancreas_sub, db = "MSigDB", group_by = "CellType", plot_type = "comparison")
#> Error in EnrichmentPlot(pancreas_sub, db = "MSigDB", group_by = "CellType",     plot_type = "comparison"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "MSigDB_MH", group_by = "CellType", plot_type = "comparison")
#> Error in EnrichmentPlot(pancreas_sub, db = "MSigDB_MH", group_by = "CellType",     plot_type = "comparison"): No enrichment result found. You may perform RunEnrichment first.

# Remove redundant GO terms
pancreas_sub <- RunEnrichment(srt = pancreas_sub, group_by = "CellType", db = "GO_BP", GO_simplify = TRUE, species = "Mus_musculus")
#> [2023-11-21 07:38:22.773752] Start Enrichment
#> Workers: 2
#> Species: Mus_musculus
#> Loading cached db: GO_BP version:3.17.0 nterm:16027 created:2023-11-21 07:14:20.545084
#> Convert ID types for the database: GO_BP
#> Connect to the Ensembl archives...
#> Using the 103 version of biomart...
#> Connecting to the biomart...
#> Searching the dataset mmusculus ...
#> Connecting to the dataset mmusculus_gene_ensembl ...
#> Converting the geneIDs...
#> Error in collect(., Inf): Failed to collect lazy table.
#> Caused by error in `db_collect()`:
#> ! Arguments in `...` must be used.
#> ✖ Problematic argument:
#> • ..1 = Inf
#> ℹ Did you misspell an argument name?
EnrichmentPlot(pancreas_sub, db = "GO_BP_sim", group_by = "CellType", plot_type = "comparison")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP_sim", group_by = "CellType",     plot_type = "comparison"): No enrichment result found. You may perform RunEnrichment first.

# Use a combined database
pancreas_sub <- RunEnrichment(
  srt = pancreas_sub, group_by = "CellType",
  db = c("KEGG", "WikiPathway", "Reactome", "PFAM", "MP"),
  db_combine = TRUE,
  species = "Mus_musculus"
)
#> [2023-11-21 07:38:26.610798] Start Enrichment
#> Workers: 2
#> Species: Mus_musculus
#> Loading cached db: MP version:2023-11-20 08:08 nterm:10311 created:2023-11-21 07:14:35.012367
#> Preparing database: KEGG
#> Preparing database: WikiPathway
#> Preparing database: Reactome
#> Preparing database: PFAM
#> Convert ID types for the database: KEGG
#> Connect to the Ensembl archives...
#> Using the 103 version of biomart...
#> Connecting to the biomart...
#> Searching the dataset mmusculus ...
#> Connecting to the dataset mmusculus_gene_ensembl ...
#> Converting the geneIDs...
#> Error in collect(., Inf): Failed to collect lazy table.
#> Caused by error in `db_collect()`:
#> ! Arguments in `...` must be used.
#> ✖ Problematic argument:
#> • ..1 = Inf
#> ℹ Did you misspell an argument name?
EnrichmentPlot(pancreas_sub, db = "Combined", group_by = "CellType", plot_type = "comparison")
#> Error in EnrichmentPlot(pancreas_sub, db = "Combined", group_by = "CellType",     plot_type = "comparison"): No enrichment result found. You may perform RunEnrichment first.

# Or use "geneID" and "geneID_groups" as input to run enrichment
de_df <- dplyr::filter(pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox, p_val_adj < 0.05)
enrich_out <- RunEnrichment(geneID = de_df[["gene"]], geneID_groups = de_df[["group1"]], db = "GO_BP", species = "Mus_musculus")
#> [2023-11-21 07:38:54.922648] Start Enrichment
#> Workers: 2
#> Species: Mus_musculus
#> Loading cached db: GO_BP version:3.17.0 nterm:16027 created:2023-11-21 07:14:20.545084
#> Convert ID types for the database: GO_BP
#> Connect to the Ensembl archives...
#> Using the 103 version of biomart...
#> Connecting to the biomart...
#> Searching the dataset mmusculus ...
#> Connecting to the dataset mmusculus_gene_ensembl ...
#> Converting the geneIDs...
#> Error in collect(., Inf): Failed to collect lazy table.
#> Caused by error in `db_collect()`:
#> ! Arguments in `...` must be used.
#> ✖ Problematic argument:
#> • ..1 = Inf
#> ℹ Did you misspell an argument name?
EnrichmentPlot(res = enrich_out, db = "GO_BP", plot_type = "comparison")
#> Error in eval(expr, envir, enclos): object 'enrich_out' not found

Perform the enrichment analysis (over-representation) on the genes

Usage

Arguments

Value

See also

Examples