Gene ontology enrichment analysis of a ranked gene list with clusterProfiler. Genes can be ranked by variance decomposition results.
Usage
enrichGO_rank(
rank_table,
gene_rank_by,
OrgDb,
keyType = "SYMBOL",
go_rank_by = "p.adjust",
category = NULL,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
...
)Arguments
- rank_table
A data frame with at least two columns: 'Feature' for gene names and one or more columns of variables for ranking the genes, e.g. output of
decomp_variance()containing variance decomposition results- gene_rank_by
Variable in
rank_tableto rank the genes by, e.g. "Time", "Group" in the output ofdecomp_variance()- OrgDb
Organism database, e.g. org.Hs.eg.db, org.Mm.eg.db
- keyType
(Optional) Available options are
AnnotationDbi::keytypes(OrgDb)(default is "SYMBOL")- go_rank_by
(Optional) Variable in the GO enrichment result to rank the GO terms by (default is "p.adjust", other options include "pvalue", "qvalue", "NES", "setSize", "enrichmentScore", etc.)
- category
(Optional) GO category to analyze (default is all three of BP, MF, CC)
- pvalueCutoff
(Optional) Parameter of
clusterProfiler::gseGO()(default is 0.05)- pAdjustMethod
(Optional) Parameter of
clusterProfiler::gseGO()(default is "BH")- ...
additional arguments passed to
clusterProfiler::gseGO()
Examples
library(org.Mm.eg.db)
data("example")
example_obj <- normalise_to_start(example_obj)
var_decomp <- decomp_variance(example_obj, assay = 1)
#>
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example_go_rank <- enrichGO_rank(var_decomp, gene_rank_by = "Time",
OrgDb = org.Mm.eg.db, keyType = "SYMBOL", category = "BP")
#> NA / NaN / Inf values found in the gene ranking variable. Those genes will be removed.
#> Warning: There are ties in the preranked stats (1.03% of the list). The order of those tied genes will be arbitrary, which may produce unexpected results.
#> Warning: There were 4821 pathways for which P-values were not calculated properly due to unbalanced gene-level statistic values. For such pathways pvalue, NES and log2err are set to NA. You can try to increase nPermSimple.
#> Warning: Invalid p-values detected (NA, non-finite, <0, or >1). qvalue will be computed on valid p-values only.
#> Warning: NA values detected in gene set IDs. Replacing with string 'NA'.
#> Warning: Duplicate gene set IDs detected: NA... (Total 1). Unique suffixes added.
#> Removing NA ID gene sets.
enrichplot::gseaplot2(example_go_rank, geneSetID = 1:2)
