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. See `CTDdata`'s detail section for more information (`?`CTDdata-class``). representation.
`representation` | Can take values `"heatmap"` or `"network"`.

### Details

`CTDdata` objects provides with a summarized representation of the downloaded data obtained from the standard `show` method. For instance, a `CTDdata` created using `query_ctd_chem` shows:
`Object of class 'CTDdata'`
`-------------------------`
`. Type: CHEMICAL`
`. Creation (timestamp): 2018-03-13 13:11:50`
`. Length: 2`
`. Items: IRON, ..., AIR POLLUTANTS`
`. Diseases: 1755 ( 203 / 3322 )`
`. Chemical-gene interactions: 2070 ( 2799 )`
`. KEGG pathways: 637 ( 637 )`
`. GO terms: 3641 ( 3641 )`
The information shows corresponds to:

- Type: Indicates the source (chemical, gene or disease) used to create the object.

- Creation: Shows the time-stamp from the creation time.

- Length: Shows the number of terms used to create the object.

- Items: Shows some of the terms used to create the object.

- Diseases: Corresponds to the unique number of diseases obtained in the query. In parenthesis: number of curated chemical-diseases and total number of chemical-diseases association.

- Chemical-gene interactions: Indicates the unique number of chemical-gene interactions. In parenthesis the total number of chemical-gene interactions.

- KEGG pathways: Shows the unique number of KEGG pathway versus chemical associations. In parenthesis the total number of associations.

- GO terms: Shows the unique number of GO terms versus chemical associations. In parenthesis the total number of associations.

`CTDdata` objects allows many types of representation according to the different sources (chemical, gene or disease). The used method is `plot`, matching the argument `x` with a `CTDdata` object. The argument `index_name` indicates the type of plot to be draw. The default value of `index_name` is `"base"`.

- `"base"`: shows a bar-plot indicating the number of lost & found terms for the given object.

For gene queries, `index_name` can take values:

- `"disease"`: (argument `representation` must be `"heatmap"`) shows shows the inference score that associates the given genes with diseases according to CTDbase.

- `"chemical interactions"`: (argument `representation` must be `"heatmap"`) shows the number of reference that cites the association between the given genes and chemicals.

- `"gene-gene interaction"`: (argument `representation` can be `"network"` and `"heatmap"`) in the network representation teh original genes are dark-colored while the other genes are light-colored. Both plots allows to to explore the gene-gene interactions.

- `"kegg pathways"`: (argument `representation` must be `"network"`) shows the linked between genes and KEGG pathways.

- `"go terms"`: (argument `representation` must be `"network"`) shows the links between genes and GO terms.

For chemical queries, `index_name` can take values:

- `"gene interactions"`: (argument `representation` can be `"network"` and `"heatmap"`) shows the gene-chemical interactions. Network representation includes the "mechanism" of the interactions.

- `"disease"`: (argument `representation` can be `"network"` and `"heatmap"`) shows the inference score of the link between chemicals and diseases.

- `"kegg pathways"`: (argument `representation` must be `"network"`) shows the P-Value of relation between KEGG pathways and chemicals.

- `"go terms"`: (argument `representation` must be `"network"`) shows the P-Value of relation between GO terms and chemicals.

For disease queries, `index_name` can take values:

- `"gene"`: (argument `representation` must be `"heatmap"`) shows the number of references linking a set of genes with a set of diseases.

- `"chemical"`: (argument `representation` must be `"heatmap"`): shows the inference-score linking diseases with chemicals.

- `"kegg pathways"`: (argument `representation` must be `"network"`) shows the pathways linked to a set of diseases.

The other arguments of `plot` functions follows:

- `subset.chemical`: filters the chemicals to be include into the plot.

- `subset.gene`: filters the genes to be include into the plot.

- `subset.pathway`: filters the KEGG pathways or GO terms included into the plot.

- `subset.source`: filters the origin in gene-gene interaction network.

- `subset.target`: filters the end in gene-gene interaction network.

- `field.score`: can take values `"Inference"` or `"Reference"` depending of the used source and representation.

- `filter.score`: allows to filter the relations to be included into the plot in base of the set of `field.score`.

- `max.length`: indicates the maximum number of characters of the names of each "item" in the plot.

- `ontology`: for the KEGG pathways, allows to filter the pathways in base of their ontology. By default: `c("Biological Process", "Cellular Component", "Molecular Function" )`.

- `main`: title to be displayed in network representations. For heatmap representations use: `+ ggtitle("TITLE")`.

### 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

`timestamp`

  Character with the timestamp.

`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 relation of the GO terms affected 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 retrieve encapsulated data and `plot` to get nice plots from stored data.

[Package CTDquerier version 2.2.0 Index]