RGo {esATAC} | R Documentation

## 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)

[Package esATAC version 1.8.0 Index]