get_anno,snp_info,pathway_info-method {kangar00}

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

See Also

snp_info, pathway_info

Examples

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