enrichGO_run: Enrichment analysis of go

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

Enrichment analysis of go

Description

run enrich_go and plot results

Usage

enrichGO_run(
  deg_data,
  x,
  y,
  cut_FC = 1,
  cut_P = 0.05,
  showCategory = 10,
  dir = ".",
  prefix = "3-EnrichGO",
  OrgDb = "org.Hs.eg.db",
  keyType = "SYMBOL",
  ont = "ALL",
  simplify = TRUE,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500,
  readable = FALSE,
  pool = FALSE,
  label = c("Down", "Stable", "Up"),
  label_ns = "Stable",
  mc.cores = 1L
)

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
showCategory	Category numbers to show
dir	where to save results files
prefix	a prefix of file names in this step
OrgDb	OrgDb
keyType	keytype of input gene
ont	One of "BP", "MF", and "CC" subontologies, or "ALL" for all three.
simplify	whether simplify
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
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.
minGSSize	minimal size of genes annotated by Ontology term for testing.
maxGSSize	maximal size of genes annotated for testing
readable	whether mapping gene ID to gene Name
pool	If ont='ALL', whether pool 3 GO sub-ontologies
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

Value

a list result files of GO

Examples

## Not run: 
enrichGO_run(DEG_df, x = "log2FoldChange", y = "pvalue", dir = tempdir())

## End(Not run)

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