R: Class CTDdata

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.