kangar00: get_anno-snp_info-pathway_info-method – R documentation

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get_anno-snp_info-pathway_info-method

Annotates SNPs via genes to pathways

Description

A function to create the annotation for a GWASdata object. It combines a snp_info and a pathway_info object into an annotation data.frame used for pathway analysis on GWAS. SNPs are assigned to pathways via gene membership.

Usage

## S4 method for signature 'snp_info,pathway_info'
get_anno(object1, object2, ...)

Arguments

`object1`	A `snp_info` object with SNP information as returned by the `snp_info` function. The included `data frame` contains the columns 'chr', 'position' and 'snp'.
`object2`	A `pathway_info` object with information on genes contained in pathways. It is created by the `pathway_info` function and contains a `data frame` with columns 'pathway', 'gene_start', 'gene_end', 'chr', 'gene'.
`...`	further argdata(hsa04020)

Value

A data.frame mapping SNPs to genes and genes to pathways. It includes the columns 'pathway', 'gene', 'chr', 'snp' and 'position'.

Author(s)

Stefanie Friedrichs, Saskia Freytag, Ngoc-Thuy Ha

Examples

data(hsa04022_info)  # pathway_info('hsa04020')
data(rs10243170_info)# snp_info("rs10243170")
get_anno(rs10243170_info, 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