SPA

SPA - SNP based pathway analysis

Description:

SPA is an R package which can identify disease or phenotype related pathways. Input rs# and GWAS test p-values, you can get the related pathways.

Maintainer:

Yongshuai Jiang: jiangyongshuai@gmail.com ; Guiyou Liu: liuguiyou1981@163.com

Download:

SPA software: http://sourceforge.net/projects/spa-software/files/SPA_1.0.tar.gz/download

Example data (snp2p.txt): http://sourceforge.net/projects/spa-software/files/snp2p.rar/download

Functions:

SPAhyper: Identifying disease or phenotype related pathways using the Hypergeometric test.
SPAfisher: Identifying disease or phenotype related pathways using the Fisher's exact test.
ShowTestResults: Show test results.
ShowDetailInfo: Show detailed information.
EnrichFisher: Fisher's exact test for SNP enrichment analysis.
EnrichHyper: Hypergeometric test for SNP enrichment analysis.
KEGG2gene: KEGG to gene
KEGG_ID_name: KEGG pathway ID and pathway name
snp2KEGGgene: SNP to KEGG gene

Examples

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!/usr/bin/R

---- Examples ----

If you have a GWAS file, which includes two solumns: column 1 rs# and column 2 p-value of GWAS.

You can download the example data "snp2p" from our website.

GWASfile=read.table("c:/snp2p.txt")

"GWASfile" is a data.frame, and include two columns.

You can use "dim(GWASfile)" to view the dimensions of "GWASfile".

In some cases, you can use "GWASfile=read.table("c:/snp2p.txt",sep="\t",quote='')" to import data.

Results=SPAhyper(SNPdata=GWASfile,SNPThreshold=0.01,BackGround='GWAS',PathwaySNPatleast=10)

This program will run for about 40 seconds to a minute.

Show test results:

Results$TestResults

or

ShowTestResults(Results)

Show detail information:

Results$detail_info[["hsa05212"]]

or

ShowDetailInfo(Results,PathwayID="hsa05212")

Show the significant SNPs annoted in the gene "6546".

ShowDetailInfo(Results,PathwayID="hsa05212",EntrezGeneID="108")
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[other].

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Project Admins:

• liuguiyou
• bioinformatics