GO enrichment analysis based on GO annotation results (None/Exist Reference Genome).
Source:R/go_enrich.R
go_enrich.RdGO enrichment analysis based on GO annotation results (None/Exist Reference Genome).
Usage
go_enrich(
go_anno,
degs_list,
padjust_method = "fdr",
pvalue_cutoff = 0.05,
qvalue_cutoff = 0.05
)Arguments
- go_anno
Dataframe: GO and KEGG annotation of background genes (1st-col: Genes, 2nd-col: biological_process, 3rd-col: cellular_component, 4th-col: molecular_function, 5th-col: kegg_pathway).
- degs_list
Dataframe: degs list.
- padjust_method
Character: P-value adjust to Q-value. Default: "fdr" (false discovery rate), options: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
- pvalue_cutoff
Numeric: P-value cutoff. Recommend: small than 0.05.
- qvalue_cutoff
Numeric: Q-value cutoff. Recommend: small than 0.05.
Value
Table: include columns ("ID", "ontology", "Description", "GeneRatio", "BgRatio", "pvalue", "p.adjust", "qvalue", "geneID", "Count").
Examples
# 1. Library TOmicsVis package
library(TOmicsVis)
# 2. Use example dataset
data(gene_go_kegg)
head(gene_go_kegg)
#> Genes
#> 1 FN1
#> 2 14-3-3ZETA
#> 3 A1I3
#> 4 A2M
#> 5 AARS
#> 6 ABAT
#> biological_process
#> 1 GO:0003181(atrioventricular valve morphogenesis);GO:0003128(heart field specification);GO:0001756(somitogenesis)
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 GO:0006419(alanyl-tRNA aminoacylation)
#> 6 GO:0009448(gamma-aminobutyric acid metabolic process)
#> cellular_component
#> 1 GO:0005576(extracellular region)
#> 2 <NA>
#> 3 GO:0005615(extracellular space)
#> 4 GO:0005615(extracellular space)
#> 5 GO:0005737(cytoplasm)
#> 6 <NA>
#> molecular_function
#> 1 <NA>
#> 2 GO:0019904(protein domain specific binding)
#> 3 GO:0004866(endopeptidase inhibitor activity)
#> 4 GO:0004866(endopeptidase inhibitor activity)
#> 5 GO:0004813(alanine-tRNA ligase activity);GO:0005524(ATP binding);GO:0000049(tRNA binding);GO:0008270(zinc ion binding)
#> 6 GO:0003867(4-aminobutyrate transaminase activity);GO:0030170(pyridoxal phosphate binding)
#> kegg_pathway
#> 1 ko04810(Regulation of actin cytoskeleton);ko04510(Focal adhesion);ko04151(PI3K-Akt signaling pathway);ko04512(ECM-receptor interaction)
#> 2 ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hippo signaling pathway);ko04391(Hippo signaling pathway -fly);ko04013(MAPK signaling pathway - fly);ko04151(PI3K-Akt signaling pathway);ko04212(Longevity regulating pathway - worm)
#> 3 ko04610(Complement and coagulation cascades)
#> 4 ko04610(Complement and coagulation cascades)
#> 5 ko00970(Aminoacyl-tRNA biosynthesis)
#> 6 ko00250(Alanine, aspartate and glutamate metabolism);ko00280(Valine, leucine and isoleucine degradation);ko00650(Butanoate metabolism);ko00640(Propanoate metabolism);ko00410(beta-Alanine metabolism);ko04727(GABAergic synapse)
# 3. Default parameters
res <- go_enrich(gene_go_kegg[,-5], gene_go_kegg[100:200,1])
head(res)
#> ID ontology
#> 1 GO:0000221 cellular component
#> 2 GO:0000275 cellular component
#> 3 GO:0000276 cellular component
#> 4 GO:0000398 biological process
#> 5 GO:0000774 molecular function
#> 6 GO:0001671 molecular function
#> Description
#> 1 vacuolar proton-transporting V-type ATPase, V1 domain
#> 2 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1
#> 3 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o
#> 4 mRNA splicing, via spliceosome
#> 5 adenyl-nucleotide exchange factor activity
#> 6 ATPase activator activity
#> GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
#> 1 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> 2 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> 3 6/101 6/1279 1.00000000 12.6633663 8.3818292 2.109128e-07
#> 4 1/101 14/1279 0.07142857 0.9045262 -0.1051372 6.858207e-01
#> 5 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> 6 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> p.adjust qvalue geneID Count
#> 1 1.110997e-01 9.458955e-02 ATP6V1H 1
#> 2 1.110997e-01 9.458955e-02 ATP5F1E 1
#> 3 1.075656e-05 9.158058e-06 ATP5MC1/ATP5ME/ATP5MG/ATP5PB/ATP5PD/ATP5PF 6
#> 4 7.363549e-01 6.269275e-01 CDC40 1
#> 5 1.110997e-01 9.458955e-02 BAG2 1
#> 6 1.110997e-01 9.458955e-02 ATP1B1 1
# 4. Set padjust_method = "BH"
res <- go_enrich(gene_go_kegg[,-5], gene_go_kegg[100:200,1], padjust_method = "BH")
head(res)
#> ID ontology
#> 1 GO:0000221 cellular component
#> 2 GO:0000275 cellular component
#> 3 GO:0000276 cellular component
#> 4 GO:0000398 biological process
#> 5 GO:0000774 molecular function
#> 6 GO:0001671 molecular function
#> Description
#> 1 vacuolar proton-transporting V-type ATPase, V1 domain
#> 2 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1
#> 3 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o
#> 4 mRNA splicing, via spliceosome
#> 5 adenyl-nucleotide exchange factor activity
#> 6 ATPase activator activity
#> GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
#> 1 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> 2 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> 3 6/101 6/1279 1.00000000 12.6633663 8.3818292 2.109128e-07
#> 4 1/101 14/1279 0.07142857 0.9045262 -0.1051372 6.858207e-01
#> 5 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> 6 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> p.adjust qvalue geneID Count
#> 1 1.110997e-01 9.458955e-02 ATP6V1H 1
#> 2 1.110997e-01 9.458955e-02 ATP5F1E 1
#> 3 1.075656e-05 9.158058e-06 ATP5MC1/ATP5ME/ATP5MG/ATP5PB/ATP5PD/ATP5PF 6
#> 4 7.363549e-01 6.269275e-01 CDC40 1
#> 5 1.110997e-01 9.458955e-02 BAG2 1
#> 6 1.110997e-01 9.458955e-02 ATP1B1 1
# 5. Set pvalue_cutoff = 0.10
res <- go_enrich(gene_go_kegg[,-5], gene_go_kegg[100:200,1], pvalue_cutoff = 0.10)
head(res)
#> ID ontology
#> 1 GO:0000221 cellular component
#> 2 GO:0000275 cellular component
#> 3 GO:0000276 cellular component
#> 4 GO:0000398 biological process
#> 5 GO:0000774 molecular function
#> 6 GO:0001671 molecular function
#> Description
#> 1 vacuolar proton-transporting V-type ATPase, V1 domain
#> 2 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1
#> 3 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o
#> 4 mRNA splicing, via spliceosome
#> 5 adenyl-nucleotide exchange factor activity
#> 6 ATPase activator activity
#> GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
#> 1 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> 2 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> 3 6/101 6/1279 1.00000000 12.6633663 8.3818292 2.109128e-07
#> 4 1/101 14/1279 0.07142857 0.9045262 -0.1051372 6.858207e-01
#> 5 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> 6 1/101 1/1279 1.00000000 12.6633663 3.4151671 7.896794e-02
#> p.adjust qvalue geneID Count
#> 1 1.110997e-01 9.458955e-02 ATP6V1H 1
#> 2 1.110997e-01 9.458955e-02 ATP5F1E 1
#> 3 1.075656e-05 9.158058e-06 ATP5MC1/ATP5ME/ATP5MG/ATP5PB/ATP5PD/ATP5PF 6
#> 4 7.363549e-01 6.269275e-01 CDC40 1
#> 5 1.110997e-01 9.458955e-02 BAG2 1
#> 6 1.110997e-01 9.458955e-02 ATP1B1 1