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###
###        README for the  
###       Supplemental Code                
###               
###              to 
###   Pathway-Based Kernel Boosting 
###  for the Analysis of Genome-Wide 
###       Association Studies
###
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### Authors:

Stefanie Friedrichs, Juliane Manitz, Patricia Burger1, Christopher I. Amos, Angela Risch,
 Jenny Chang-Claude, H.-Erich Wichmann, Thomas Kneib, Heike Bickeboeller, and Benjamin Hofner

### Contact (for questions regarding the code):

Stefanie Friedrichs <sfriedr2@gwdg.de>
Benjamin Hofner <benjamin.hofner@pei.de>


### About the example code: 

The following data can be used to run an exemplary analysis using the kernel boosting method. Genetic information supplied does not affect provided phenotypes (null case).

Information on how to derive the necessary information from online databases is given in the example code for some of the datasets. Thus, the corresponding information can either be downloaded directly or loaded from the supplied data files. 

The R-packages kangar00 and mboost are needed to perform kernel boosting.  



### Data: 

# genotype.data.Rda: 
simulated, non-influential genotypes in minor allele coding (0, 1 or 2) for 17,972 genetic markers and 200 individuals


# snps.Rda:
rs-number identifiers of the 17,972 SNPs for which genotypes are given in the genotype.data.Rda file
 

# phenotype.data.Rda:
simulated, non-influential phenotypes for the 200 individuals included in the genotype file; information on case control status, sex and age is included


# list.of.pathways.Rda: 
includes 5 exemplary pathway objects created in the kangar00 package. Information on gene interaction was derived from the KEGG database in April 2017 


# pathway.info.Rda: 
information on 499 genes included in at least one of the 5 example pathways. For each gene the name, the genomic location (start and end position in base pairs), the chromosome, and the pathway in which it is included in are given. All information was derived from the Ensembl database in April 2017.


# snp.info.Rda: 
information on SNPs contined in the genes of the 5 example pathways. For each marker the rs.number, chromosome and base pair position are given. The information was derived from the Ensembl database in April 2017.



### Code:

The corresponding analysis code was prepared by Benjmain Hofner and Stefanie Friedrichs.



This README file was written by: Stefanie Friedrichs.
