enrichKEGG_run: Enrichment analysis of kegg

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

Enrichment analysis of kegg

Description

run enrich_kegg and plot results

Usage

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

## Not run: 
enrichKEGG_run(deg_data = DEG_df, x = "log2FoldChange", y = "pvalue", cut_FC = 1,
cut_P = 0.05, top = -10)

## End(Not run)

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