MixMAP (version 1.3.4)

MixMAP_example: A working example of the MixMAP algorithm.

Description

Data containing the results of a meta-analysis consisting of many GWAS whose phenotype of interest is LDL cholesterol. This file contains all of the information necessary to run the MixMAP function directly without any pre-processing.

Usage

data(MixMAP_example)

Format

A data frame with 31825 observations and the following five variables: MarkerName: a character with SNP name GC.Pvalue: a numeric with p-values for each SNP Coordinate: integer containing the base pair location of the SNP within the chromosome Chr: integer containing the chromsome number of the SNP Gene: A character with gene symbol

Source

Nature 466, 707--713 (05 August 2010) The p-values in this file are from the paper Teslovich Et Al. (2009) ``Biological, clinical and population relevance of 95 loci for blood lipids" Nature 466: 707--713. The phenotype of interest was low-density lipoprotein (LDL) cholesterol. The SNPs chosen are a subset that are found in the IBC array and have a unique gene name associated with them.

Details

This file contains all of the information needed to run the MixMAP function directly.

References

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.

Examples

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)