pathway_info: An S4 class for an object assigning genes to pathways
Description
This function lists all genes formig a particular pathway. Start and end
positions of these genes are extracted from the Ensemble database. The
database is accessed via the R-package biomaRt.
Usage
pathway_info(x)
# S4 method for character
pathway_info(x)
# S4 method for pathway_info
show(object)
# S4 method for pathway_info
summary(object)
Value
A data.frame including as many rows as genes appear in the
pathway. for each gene its name, the start and end point and the chromosome
it lies on are given.
show Basic information on pathway_info object.
summary Summarized information on pathway_info object.
Arguments
x
A character identifying the pathway for which gene infomation
should be extracted. Here KEGG IDs (format: 'hsa00100') are used.
object
An object of class pathway_info.
Slots
info
A data.frame including information on genes contained in
pathways with columns 'pathway', 'gene_start', 'gene_end', 'chr' and 'gene'.