Description Usage Format Details Source References Examples
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.
1 |
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
This file contains all of the information needed to run the MixMAP function directly.
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.
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 13 | 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)
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'data.frame': 31825 obs. of 5 variables:
$ MarkerName: chr "rs10" "rs10000405" "rs10000679" "rs10000850" ...
$ Gene : Factor w/ 2960 levels "2-Sep","A1BG",..: 497 603 2879 1887 1381 801 2902 2902 1465 1937 ...
$ Chr : int 7 4 4 4 5 9 4 4 19 4 ...
$ Coordinate: int 92221824 47411638 177907958 56195135 150220269 112834321 6335534 6327482 16310517 164462801 ...
$ GC.Pvalue : num 0.0403 0.5013 0.1195 0.5547 0.394 ...
Length Class Mode
1 MixMAP S4
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