CTDdata-class: Class CTDdata

In CTDquerier: Package for CTDbase data query, visualization and downstream analysis

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.

CTDquerier documentation built on Oct. 31, 2019, 2:57 a.m.