RGo: Gene Ontology Analysis

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

Gene Ontology Analysis

Description

Ranking functional groups based on a set of genes. For more information, please see enrichGO.

Usage

atacGOAnalysis(
  atacProc,
  gene = NULL,
  OrgDb = NULL,
  keytype = "ENTREZID",
  ont = "MF",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe = NULL,
  qvalueCutoff = 0.2,
  readable = FALSE,
  pool = FALSE,
  goOutput = NULL,
  ...
)

## S4 method for signature 'ATACProc'
atacGOAnalysis(
  atacProc,
  gene = NULL,
  OrgDb = NULL,
  keytype = "ENTREZID",
  ont = "MF",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe = NULL,
  qvalueCutoff = 0.2,
  readable = FALSE,
  pool = FALSE,
  goOutput = NULL,
  ...
)

goanalysis(
  gene,
  OrgDb = NULL,
  keytype = "ENTREZID",
  ont = "MF",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe = NULL,
  qvalueCutoff = 0.2,
  readable = FALSE,
  pool = FALSE,
  goOutput = NULL,
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacPeakAnno.
gene	A vector of entrez gene id.
OrgDb	Genome wide annotation databese.
keytype	Keytype of input gene.
ont	One of "MF", "BP", and "CC" subontologies. "MF" for molecular function, "BP" for biological process, "CC" for cellular component.
pvalueCutoff	pvalueCutoff.
pAdjustMethod	One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
universe	Background genes.
qvalueCutoff	qvalue cutoff.
readable	whether mapping gene ID to gene Name.
pool	If ont=’ALL’, whether pool 3 GO sub-ontologies.
goOutput	Character scalar. Output file path. Defult:in the same folder as your input file with the suffix "df".
...	Additional arguments, currently unused.

Details

This function using enrichGO to do GO analysis but fixed some parameters. If atacProc is not NULL, it will read the gene ID from the output of atacPeakAnno.

Value

An invisible ATACProc-class object scalar.

Author(s)

Wei Zhang

References

Guangchuang Yu., Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287

See Also

atacPeakAnno enrichGO function enrichGO in package "clusterProfiler"

Examples

## Not run: 
library(org.Hs.eg.db)
# generate simulated geneID
geneId <- as.character(sample(seq(10000), 100))
goanalysis(gene = geneId, OrgDb = 'org.Hs.eg.db')

## End(Not run)

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.