KEGG enrichment analysis based on KEGG annotation results (None/Exist Reference Genome).
Source:R/kegg_enrich.R
kegg_enrich.RdKEGG enrichment analysis based on KEGG annotation results (None/Exist Reference Genome).
Usage
kegg_enrich(
kegg_anno,
degs_list,
padjust_method = "fdr",
pvalue_cutoff = 0.05,
qvalue_cutoff = 0.05
)Arguments
- kegg_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", "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 <- kegg_enrich(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1])
#> Warning: Expected 2 pieces. Additional pieces discarded in 27 rows [695, 696, 744, 747,
#> 750, 968, 977, 1177, 1474, 1646, 1653, 1659, 1886, 2163, 2174, 2187, 2193,
#> 2198, 2258, 2259, ...].
head(res)
#> ID Description GeneRatio BgRatio
#> ko04966 ko04966 Collecting duct acid secretion 7/101 7/1279
#> ko00190 ko00190 Oxidative phosphorylation 23/101 88/1279
#> ko04721 ko04721 Synaptic vesicle cycle 8/101 13/1279
#> ko04610 ko04610 Complement and coagulation cascades 13/101 43/1279
#> ko04145 ko04145 Phagosome 11/101 33/1279
#> ko04971 ko04971 Gastric acid secretion 4/101 4/1279
#> pvalue p.adjust qvalue
#> ko04966 1.573976e-08 2.030430e-06 1.723090e-06
#> ko00190 5.232645e-08 3.375056e-06 2.864185e-06
#> ko04721 1.069634e-06 4.599427e-05 3.903227e-05
#> ko04610 1.078094e-05 3.476853e-04 2.950573e-04
#> ko04145 1.941460e-05 5.008968e-04 4.250776e-04
#> ko04971 3.679084e-05 7.910030e-04 6.712714e-04
#> geneID
#> ko04966 ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/CA1
#> ko00190 ATP5F1A/ATP5F1B/ATP5F1C/ATP5F1D/ATP5F1E/ATP5MC1/ATP5MC2/ATP5MC3/ATP5ME/ATP5MF/ATP5MG/ATP5PB/ATP5PD/ATP5PF/ATP5PO/ATP6V0B/ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/ATP6V1H
#> ko04721 ATP6V0B/ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/ATP6V1H
#> ko04610 C1QC/C1S/C3/C4/C4A/C5/C6/C7/C8A/C8B/C8G/C9/CD59
#> ko04145 ATP6V0B/ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/ATP6V1H/C3/CALR/CANX
#> ko04971 ATP1B1/CA1/CALM1/CAMK2D
#> Count
#> ko04966 7
#> ko00190 23
#> ko04721 8
#> ko04610 13
#> ko04145 11
#> ko04971 4
# 4. Set padjust_method = "BH"
res <- kegg_enrich(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1], padjust_method = "BH")
#> Warning: Expected 2 pieces. Additional pieces discarded in 27 rows [695, 696, 744, 747,
#> 750, 968, 977, 1177, 1474, 1646, 1653, 1659, 1886, 2163, 2174, 2187, 2193,
#> 2198, 2258, 2259, ...].
head(res)
#> ID Description GeneRatio BgRatio
#> ko04966 ko04966 Collecting duct acid secretion 7/101 7/1279
#> ko00190 ko00190 Oxidative phosphorylation 23/101 88/1279
#> ko04721 ko04721 Synaptic vesicle cycle 8/101 13/1279
#> ko04610 ko04610 Complement and coagulation cascades 13/101 43/1279
#> ko04145 ko04145 Phagosome 11/101 33/1279
#> ko04971 ko04971 Gastric acid secretion 4/101 4/1279
#> pvalue p.adjust qvalue
#> ko04966 1.573976e-08 2.030430e-06 1.723090e-06
#> ko00190 5.232645e-08 3.375056e-06 2.864185e-06
#> ko04721 1.069634e-06 4.599427e-05 3.903227e-05
#> ko04610 1.078094e-05 3.476853e-04 2.950573e-04
#> ko04145 1.941460e-05 5.008968e-04 4.250776e-04
#> ko04971 3.679084e-05 7.910030e-04 6.712714e-04
#> geneID
#> ko04966 ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/CA1
#> ko00190 ATP5F1A/ATP5F1B/ATP5F1C/ATP5F1D/ATP5F1E/ATP5MC1/ATP5MC2/ATP5MC3/ATP5ME/ATP5MF/ATP5MG/ATP5PB/ATP5PD/ATP5PF/ATP5PO/ATP6V0B/ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/ATP6V1H
#> ko04721 ATP6V0B/ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/ATP6V1H
#> ko04610 C1QC/C1S/C3/C4/C4A/C5/C6/C7/C8A/C8B/C8G/C9/CD59
#> ko04145 ATP6V0B/ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/ATP6V1H/C3/CALR/CANX
#> ko04971 ATP1B1/CA1/CALM1/CAMK2D
#> Count
#> ko04966 7
#> ko00190 23
#> ko04721 8
#> ko04610 13
#> ko04145 11
#> ko04971 4
# 5. Set pvalue_cutoff = 0.80
res <- kegg_enrich(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1], pvalue_cutoff = 0.80)
#> Warning: Expected 2 pieces. Additional pieces discarded in 27 rows [695, 696, 744, 747,
#> 750, 968, 977, 1177, 1474, 1646, 1653, 1659, 1886, 2163, 2174, 2187, 2193,
#> 2198, 2258, 2259, ...].
head(res)
#> ID Description GeneRatio BgRatio
#> ko04966 ko04966 Collecting duct acid secretion 7/101 7/1279
#> ko00190 ko00190 Oxidative phosphorylation 23/101 88/1279
#> ko04721 ko04721 Synaptic vesicle cycle 8/101 13/1279
#> ko04610 ko04610 Complement and coagulation cascades 13/101 43/1279
#> ko04145 ko04145 Phagosome 11/101 33/1279
#> ko04971 ko04971 Gastric acid secretion 4/101 4/1279
#> pvalue p.adjust qvalue
#> ko04966 1.573976e-08 2.030430e-06 1.723090e-06
#> ko00190 5.232645e-08 3.375056e-06 2.864185e-06
#> ko04721 1.069634e-06 4.599427e-05 3.903227e-05
#> ko04610 1.078094e-05 3.476853e-04 2.950573e-04
#> ko04145 1.941460e-05 5.008968e-04 4.250776e-04
#> ko04971 3.679084e-05 7.910030e-04 6.712714e-04
#> geneID
#> ko04966 ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/CA1
#> ko00190 ATP5F1A/ATP5F1B/ATP5F1C/ATP5F1D/ATP5F1E/ATP5MC1/ATP5MC2/ATP5MC3/ATP5ME/ATP5MF/ATP5MG/ATP5PB/ATP5PD/ATP5PF/ATP5PO/ATP6V0B/ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/ATP6V1H
#> ko04721 ATP6V0B/ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/ATP6V1H
#> ko04610 C1QC/C1S/C3/C4/C4A/C5/C6/C7/C8A/C8B/C8G/C9/CD59
#> ko04145 ATP6V0B/ATP6V0C/ATP6V0E1/ATP6V1B2/ATP6V1C1A/ATP6V1F/ATP6V1G1/ATP6V1H/C3/CALR/CANX
#> ko04971 ATP1B1/CA1/CALM1/CAMK2D
#> Count
#> ko04966 7
#> ko00190 23
#> ko04721 8
#> ko04610 13
#> ko04145 11
#> ko04971 4