get_anno,snp_info,pathway_info-method

get_anno

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

Methods to extract information on pathways, genes and various single-nucleotid polymorphisms (SNPs) from online databases. It provides functions for data preparation and evaluation of genetic influence on a binary outcome using the logistic kernel machine test (LKMT). Three different kernel functions are offered to analyze genotype information in this variance component test: A linear kernel, a size-adjusted kernel and a network-based kernel).

Juliane Manitz

kangar00

Kernel Approaches for Nonlinear Genetic Association Regression

Benjamin Hofner

Stefanie Friedrichs

Patricia Burger

Ngoc Thuy Ha

Saskia Freytag

Heike Bickeboeller

get_anno,snp_info,pathway_info-method function

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

Arguments

Stefanie Friedrichs, Saskia Freytag, Ngoc-Thuy Ha

Author

Annotates SNPs via genes to pathways — get_anno,snp_info,pathway_info-method

<dl>

<dt>object1</dt>
<dd>A <code>snp_info</code> object with SNP information as returned
by the <code>snp_info</code> function. The included <code>data frame</code> contains
the columns 'chr', 'position' and 'snp'.</dd>


<dt>object2</dt>
<dd>A <code>pathway_info</code> object with information on genes
contained in pathways. It is created by the <code>pathway_info</code> 
function and contains a <code>data frame</code> with columns 
'pathway', 'gene_start', 'gene_end', 'chr', 'gene'.</dd>


<dt>...</dt>
<dd>further argdata(hsa04020)</dd>

</dl>

get_anno,snp_info,pathway_info-method: Annotates SNPs via genes to pathways

Description

Usage

Value

Arguments

Author

See Also

Examples