gseKEGG from DEG data

run gseKEGG. of DEG data

enrich_gsekegg(
  deg_data,
  x,
  organism = "hsa",
  keyType = "kegg",
  OrgDb = "org.Hs.eg.db",
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  eps = 1e-10,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  use_internal_data = FALSE,
  seed = FALSE,
  by = "fgsea",
  ...
)

Arguments

deg_data

a DEG data frame contains logFC and p value

x

which column is log FC

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

exponent

weight of each step

minGSSize

minimal size of each geneSet for analyzing

maxGSSize

maximal size of genes annotated for testing

eps

This parameter sets the boundary for calculating the p value.

pvalueCutoff

pvalue Cutoff

pAdjustMethod

pvalue adjustment method

verbose

print message or not

use_internal_data

logical, use KEGG.db or latest online KEGG data

seed

logical

by

one of 'fgsea' or 'DOSE'

...

other parameter

Value

a gsekegg result

Examples

if (FALSE) {
enrich_gsekegg(DEF_df,x = "log2FoldChange")
}