CMdictionary {Onassis} | R Documentation

## `CMdictionary`

### Description

Constructor method for creating instances of class `CMdictionary-class`. The created Conceptmapper dictionary will be stored as an XML file in the file system.

### Usage

    CMdictionary(inputFileOrDb = NULL, dictType = "OBO",
      outputDir = tempdir(), synonymType = "EXACT", taxID = 0,
      outputDirOp = TRUE)

### Arguments

`inputFileOrDb` | The local OBO/OWL ontology to be converted into an XML Conceptmapper dictionary or the URL of a OBO/OWL file. If inputFileOrdb is NA and the `dicType` parameter is not the generic OBO then the method tries to download the corresponding dictionary from the available repositories. For ENTREZ and TARGET dictionary types a file named gene_info.gz will be automatically downloaded from ftp://ncbi.nlm.nih.gov/gene/data/gene_info.gz if a valid path is not provided by the user. Alternatively the name of an annotation package of the type Org.xx.eg.db from Bioconductor can be used. In this case the gene unique identifiers and their alternative identifiers will be retrieved from the annotation database without the need of downloading a gene_info file.
`dictType` | the type of input dictionary OBO A dictionary that has been created by An OBO file ENTREZ Entrez genes dictionary TARGET Entrez genes dictionary, Histone marks and Histone modifications CMDICT A previously created dictionary file in the Conceptmapper XML format
`outputDir` | the directory where the XML conceptmapper dictionary will be stored. Defaults to the tmp system's directory
`synonymType` | The type of synonyms to consider when building the dictionary for Conceptmapper. For further detail http://owlcollab.github.io/oboformat/doc/obo-syntax.html. Default: EXACT EXACT ALL
`taxID` | the taxonomy identifier of the organism when the dictionary type is ENTREZ or TARGET. If 0 all the taxonomies will be included in the new dictionary.
`outputDirOp` | set to TRUE to clean the directory before creating the dictionary

### Value

An object of type `CMdictionary-class` that can be used to annotate text with the `EntityFinder`.

### Examples

    ## Not run:
    #' ##This might take some time to download the dictionary
    dict <- CMdictionary(dictType = 'TARGET', inputFileOrDb='org.Hs.eg.db')

    dict_file <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
    dictionary <- CMdictionary(dictType='OBO', inputFileOrDb=dict_file)

    ## End(Not run)

[Package Onassis version 1.2.7 Index]