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:

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".

For gene queries, index_name can take values:

For chemical queries, index_name can take values:

For disease queries, index_name can take values:

The other arguments of plot functions follows:

Value

An object of class CTDdata

Methods (by generic)

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 2.0.0 Index]