run enrichgesKEGG

run enrichgesKEGG and make output files

enrichgesKEGG_run(
  deg_data,
  x,
  dir = ".",
  prefix = "5-EnrichgseKEGG",
  pvalue_cut = 0.1,
  enrichmentScore_cut = 0.5,
  top = -10,
  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

dir

where to save results files

prefix

a prefix of file names in this step

pvalue_cut

filter by pvalue

enrichmentScore_cut

filter by enrichmentScore

top

top rows of up and down

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'

Value

a list of file

Examples

if (FALSE) {
enrichgesKEGG_run(deg_data = DEG_df, x = "log2FoldChange", dir = tempdir(),eps = 0)
}