CTDdata-class: Class CTDdata

In isglobal-brge/CTDquerier: Package for CTDbase data query, visualization and downstream analysis

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(CTDdata): Method to perform enrichment analysis given two object of class CTDdata.

• get_table(CTDdata): Method to obtain a specific inner table from an CTDdata object.

• get_terms(CTDdata): Return a list with the terms found to create the object.

• plot(x = CTDdata, y = ANY): 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.

isglobal-brge/CTDquerier documentation built on Oct. 6, 2022, 1:18 p.m.