CTDdata {CTDquerier} | R Documentation

## Class CTDdata

### Description

Class resulting of `query_ctd_gene`, `query_ctd_chem` and `query_ctd_dise`. It is used to encapsulate all the information in CTDbase for given set of genes, chemicals or diseases.

### Usage

    ## S4 method for signature 'CTDdata'
    enrich(x, y, universe, use = "curated", warnings = TRUE,
      ...)

    ## S4 method for signature 'CTDdata'
    get_table(object, index_name, ...)

    ## S4 method for signature 'CTDdata'
    get_terms(object)

    ## S4 method for signature 'CTDdata,ANY'
    plot(x, y, index_name = "base",
      representation = "heatmap", ...)

### Arguments

`x` | Object of class `CTDdata`.
`y` | NOT USED
`universe` | String vector of genes used as universe. If not provided, all genes in CTDbase are used.
`use` | Select if all or only curated relations are used.
`warnings` | Shows or hiddes warnings.
`...` | NOT USED
`object` | Object of class `CTDdata`.
`index_name` | Name of the plot to be draw. `"base"` shows a bar-plot indicating the number of terms lost&found at CTDbase. For gene queries `index_name` can take values `"disease"`, `"chemical"`, `"gene-gene interaction"`, `"kegg pathways"` and `"go terms"`. The first two have only `"heatmap"` representation, the last to have only `"network"` representation, and `"gene-gene interaction"` has both. For chemical queries `index_name` can take values `"gene"`, `"disease"`, `"kegg pathways"` and `"go terms"`. The first has both `"heatmap"` and `"network"` representation, while the last only `"network"`. The otehr three have only `"heatmap"` representation. For disease queries `index_name` can take values `"gene"`, `"chemical"` and `"kegg pathways"`. The first two have `"heatmap"` representation while the last `"network"` representation.
`representation` | Can take values `"heatmap"` or `"network"`.

### Value

An object of class `CTDdata`

### Methods (by generic)

- `enrich`: Method to perform enrichment analysis given two object of class `CTDdata`.

- `get_table`: Method to obtain a specific inner table from an `CTDdata` object.

- `get_terms`: Return a list with the terms found to create the object.

- `plot`: Generates a basic plot showing the number of terms that can be used to query CTDbase.

### Slots

`type`

  Character saving `"GENE"`, `"CHEMICAL"` or `"DISEASE"` depending if it was created using `query_ctd_gene`, `query_ctd_chem` or `query_ctd_dise`

`terms`

  `DataFrame` with the genes, chemicals or diseases used to create the object.

`losts`

  Character with the terms used to create the object but that were nor present in CTDbase.

`gene_interactions`

  (Only for chemicals) Table with a relation of the genes interacting with the given chemicals.

`chemicals_interactions`

  (Only for genes) Table with a relation of the chemicals interacting with the given genes.

`diseases`

  Table with a relation of the diseases associated with given genes or chemicals.

`gene_gene_interactions`

  (Only for genes) Table with a relation of the genes interacting with the given genes.

`kegg`

  Table with a relation of the KEGG pathways affected by the given chemicals or where the given genes play a role.

`go`

  Table with a relatio of the GO terms afected by the given chemicals or where the given genes play a role.

### See Also

`query_ctd_gene` to create a `CTDdata` from a set of genes, `query_ctd_chem` to create a `CTDdata` from a set of chemicals, `query_ctd_dise` to create a `CTDdata` from a set of diseases, `get_table` to retrive encapsulated data and `plot` to get nice plots from stored data.

[Package CTDquerier version 1.0.0 Index]