enrich_gsekegg: gseKEGG from DEG data

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

gseKEGG from DEG data

Description

run gseKEGG. of DEG data

Usage

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

## Not run: 
enrich_gsekegg(DEF_df,x = "log2FoldChange")

## End(Not run)

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