A class to store mapping information between genes, pathways and interPro domains

Description

This class represents the data necessary to run gseDomain

Details

You should always create these objects using either one of the functions dataSource or getKEGGdata.

Creating Objects

Objects can be created using
new('ipDataSource',
genes = ...., # Object of class character
pathways = .... # Object of class character
domains = .... # Object of class character
gene2Domains = .... # Object of class environment
path2Domains = .... # Object of class environment
type = ...., # Object of class character
)
or the functions dataSource or getKEGGdata.

Slots

genes:

Vector of unique entrezgene identifiers

pathways:

Vector of unique pathway identifiers

domains:

Vector of unique InterPro identifiers

gene2Domains:

Hash table mapping entrezgene IDs to Interpro IDs

path2Domains:

Hash table mapping pathway IDs to InterPro IDs

type:

Type of pathway. A character skalar

dims:

Numeric vector of dimensions

Methods

show

display summary.

Author(s)

Florian Hahne

See Also

dataSource or getKEGGdata

Results