clusterEnrichment {transcriptogramer} | R Documentation

## Term enrichment

### Description

If `species` is a character, this method uses the biomaRt package to build a Protein2GO list, if `species` is a data.frame, it will be used instead. The Protein2GO list will be used with the topGO package to detect the most significant terms of each cluster present in the DE slot of the `object`.

### Usage

    clusterEnrichment(object, universe = NULL, species,
      ontology = "biological process", algorithm = "classic",
      statistic = "fisher", pValue = 0.05, adjustMethod = "BH",
      nCores = 1L, onlyGenesInDE = FALSE)

    ## S4 method for signature 'Transcriptogram'
    clusterEnrichment(object, universe = NULL,
      species, ontology = "biological process", algorithm = "classic",
      statistic = "fisher", pValue = 0.05, adjustMethod = "BH",
      nCores = 1L, onlyGenesInDE = FALSE)

### Arguments

`object` | An object of class Transcriptogram.
`universe` | A character vector containing ENSEMBL Peptide IDs, or NULL, if the universe is composed by all the proteins present in the ordering slot of `object`.
`species` | A character string specifying the species; or a data.frame containing two columns, the first one with ENSEMBL Peptide IDs (character), which may, or not, to contain the taxonomy ID of the species as prefix, and the second containing its respective Gene Ontology term (character).
`ontology` | A character string specifying the Gene Ontology domain, ignoring case sensitivity, the possible values are 'biological process', 'cellular component' and 'molecular function'. The default value of this argument is 'biological process'.
`algorithm` | Character string specifying which algorithm to use, the possible values are 'classic', 'elim', 'weight', 'weight01', 'lea' and 'parentchild'. The default value of this argument is 'classic'.
`statistic` | Character string specifying which test to use, the possible values are 'fisher', 'ks', 't', 'sum' and 'globaltest'. The default value of this argument is 'fisher'.
`pValue` | A numeric value between 0 and 1 giving the required family-wise error rate or false discovery rate. The default value of this argument is 0.05.
`adjustMethod` | Character string specifying p-value adjustment method, the possible values are 'none', 'BH', 'fdr' (equivalent to 'BH'), 'BY', 'hochberg', 'hommel', 'bonferroni', and 'holm'. The default value of this argument is 'BH'.
`nCores` | An integer number, referring to the number of processing cores to be used; or a logical value, TRUE indicating that all processing cores should be used, and FALSE indicating the use of just one processing core. The default value of this argument is 1.
`onlyGenesInDE` | Logical value, set as TRUE to use only the genes in the DE slot. Set as FALSE to use all the genes referring to the positions in the clusters slot. The default value of this argument is FALSE.

### Value

This method creates a data.frame, containing the most significant terms of each cluster, to feed the Terms slot of an object of class Transcriptogram.

### Author(s)

Diego Morais

### See Also

differentiallyExpressed, transcriptogramPreprocess, GSE9988, GPL570, Hs900, HsBPTerms, association, transcriptogramStep1, transcriptogramStep2

### Examples

    transcriptogram <- transcriptogramPreprocess(association, Hs900, 50)
    ## Not run:
    transcriptogram <- transcriptogramStep1(transcriptogram, GSE9988, GPL570)
    transcriptogram <- transcriptogramStep2(transcriptogram)
    levels <- c(rep(FALSE, 3), rep(TRUE, 3))
    transcriptogram <- differentiallyExpressed(transcriptogram, levels, 0.01)
    transcriptogram <- clusterEnrichment(transcriptogram, species = "Homo sapiens",
    pValue = 0.005)

    ## this call also works
    transcriptogram <- clusterEnrichment(transcriptogram, species = HsBPTerms,
    pValue = 0.005)

    ## End(Not run)

[Package transcriptogramer version 1.8.0 Index]