kangar00: pathway_info-class – R documentation

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pathway_info-class

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 signature 'character'
pathway_info(x)

## S4 method for signature 'pathway_info'
show(object)

## S4 method for signature 'pathway_info'
summary(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`.

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.

Slots

info: A data.frame including information on genes contained in pathways with columns 'pathway', 'gene_start', 'gene_end', 'chr' and 'gene'.

Author(s)

Stefanie Friedrichs, Juliane Manitz

Examples

data(hsa04022_info) # pathway_info('hsa04020') 
show(hsa04022_info)
summary(hsa04022_info)

kangar00

Kernel Approaches for Nonlinear Genetic Association Regression

v1.4

GPL-2

Authors

Juliane Manitz [aut], Stefanie Friedrichs [aut], Patricia Burger [aut], Benjamin Hofner [aut], Ngoc Thuy Ha [aut], Saskia Freytag [ctb], Heike Bickeboeller [ctb]

Initial release

2020-02-12