TOmicsVis (version 2.0.0)

kegg_enrich: KEGG enrichment analysis based on KEGG annotation results (None/Exist Reference Genome).

Description

KEGG 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
)

Value

Table: include columns ("ID", "Description", "GeneRatio", "BgRatio", "pvalue", "p.adjust", "qvalue", "geneID", "Count").

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.

Author

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(gene_go_kegg)
head(gene_go_kegg)

# 3. Default parameters
res <- kegg_enrich(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1])
head(res)

# 4. Set padjust_method = "BH"
res <- kegg_enrich(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1], padjust_method = "BH")
head(res)

# 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)
head(res)