enrichgesKEGG_run: run enrichgesKEGG

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

run enrichgesKEGG

Description

run enrichgesKEGG and make output files

Usage

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

## Not run: 
enrichgesKEGG_run(deg_data = DEG_df, x = "log2FoldChange", dir = tempdir(),eps = 0)

## End(Not run)

xiayh17/RNAseqStat documentation built on June 16, 2022, 11:51 a.m.