Description Details Author(s) References See Also Examples
Mixed Modeling approach based on Meta-analysis p-values for detecting gene level associations from genome wide assocation studies (GWAS) or candidate gene studies.
This package uses raw p-values from previous GWAS, and information about gene-level groupings to search for gene-level assocations between complex disease phenotypes and genetic loci.
Package: | MixMAP |
Type: | Package |
Version: | 1.0 |
Date: | 2012-08-13 |
License: | GPL-3 |
This goal of this package is to implement the MixMAP algorithm. The aim of the algorithm is to search for assocations between genes and complex diseases by using individual SNP-level p-values. The user must provides a file with SNP name and SNP p-value as well as gene name, chromosome, and basepair location. The output of the function MixMAP is an object of class MixMAP
, which contains information on genes that have been detected as being associated with the phenotype of interest. An object of class MixMAP
has a plot method associated with it to visually display the result of the MixMAP algorithm in a Manhattan style plot as well as a summary method.
Gregory J. Matthews and Andrea Foulkes
Maintainer: Gregory J. Matthews <gjm112@gmail.com>
Foulkes, A.S., Matthews, G.J., Das, U., Ferguson, J., Reilly, M. (2013) “Mixed Modeling of Meta-Analysis P-Values (MixMAP) Suggests Multiple Novel Gene Loci for Low Density Lipoprotein Cholesterol". PLoS ONE 8(2): e54812.
Matthews, G.J. and Foulkes, A.S. (2015) “MixMAP: An R Package for Mixed Modeling of Meta-Analysis $p$ Values in Genetic Association Studies." Journal of Statistical Software. 66(3): 1-11.
1 2 3 4 5 6 7 8 9 10 11 12 | library(MixMAP)
#Load data
#This data has been prepared to be used as input to the MixMAP function directly
data(MixMAP_example)
str(MixMAP_example)
#Run mixmapTest
MixOut<-mixmapTest(MixMAP_example,pval="GC.Pvalue",snp="MarkerName",
chr="Chr",coord="Coordinate",gene="Gene")
#Display first ten detected genes
summary(MixOut)
#MixManhattan Plot
plot(MixOut)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.