Enrichment analysis of kegg — enrichKEGG

run enrich_kegg and plot results

enrichKEGG_run(
  deg_data,
  x,
  y,
  cut_FC = 1,
  cut_P = 0.05,
  top = -10,
  dir = ".",
  prefix = "4-EnrichKEGG",
  organism = "hsa",
  keyType = "kegg",
  OrgDb = "org.Hs.eg.db",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2,
  use_internal_data = FALSE,
  label = c("Down", "Stable", "Up"),
  label_ns = "Stable",
  mc.cores = 1L,
  down_label = "Down"
)

Arguments

deg_data: a DEG data frame contains logFC and p value
x: which column is log FC
y: which column is P value
cut_FC: a single number character or numeric vector in threshold value of log FC
cut_P: threshold value of P value, can set for every cut_FC number in numeric vector format
top: top rows for up and down
dir: where to save results files
prefix: a prefix of file names in this step
organism: supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html'
keyType: one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'
OrgDb: OrgDb
pvalueCutoff: adjusted pvalue cutoff on enrichment tests to report
pAdjustMethod: one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
minGSSize: minimal size of genes annotated by Ontology term for testing.
maxGSSize: maximal size of genes annotated for testing
qvalueCutoff: qvalue cutoff on enrichment tests to report as significant. Tests must pass i) pvalueCutoff on unadjusted pvalues, ii) pvalueCutoff on adjusted pvalues and iii) qvalueCutoff on qvalues to be reported.
use_internal_data: logical, use KEGG.db or latest online KEGG data
label: symbol word for groups
label_ns: which group is the stable group
mc.cores: param for mclapply, choose cores to use in non-Windows machine
down_label: which one is Down

Value

a list result files of KEGG

Examples

if (FALSE) {
enrichKEGG_run(deg_data = DEG_df, x = "log2FoldChange", y = "pvalue", cut_FC = 1,
cut_P = 0.05, top = -10)
}