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Resources related to Novembre et al (2008) Nature 456:98-101
This project forked from novembrelab/novembre_etal_2008_misc
Resources related to Novembre et al (2008) Nature 456:98-101
1/12/14 This repository contains several files that are helpful for reproducing the main figure of the Novembre et al 2008 ``Genes Mirror Geography in Europe'' paper. The raw POPRES data must be accessed via dbGAP. File descriptions: ==== Main files for plotting of PCA plot ==== PCA.txt : File with basic results for plotting ID: The individual ID plabels: Population labels alabels: Abbreviated label longitude: longitude used in study for that population latitude: latitude used in study for that population PC1: self-explanatory PC2: self-explanatory RotNS: North/South coordinate after rotation of PCA (see methods) RotEW: East/west coordinate after rotation of PCA (see methods) POPRESID_Color.txt : Color used for each individual in plot ==== Files for geographic plot ==== world_countries.rda : World polygon data ColorTablePCmap.txt : Color used for each country in the geographic inset map To generate the colored geographic map: library(sp) library(rgdal) load("world_countries.rda") coldatamap=read.table("ColorTablePCmap.txt",sep="\t",as.is=TRUE) names(coldatamap)=c("cntry","color") row.names(coldatamap)=toupper(coldatamap$cntry) plot(worldpolys,xlim=c(-8,35),ylim=c(35,60),col=coldatamap[toupper(worldpolys$names),"color"]) ===== Miscellaneous files ===== POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.bim : A .bim file in plink format describing the 197,146 markers used in the thinned dataset for the PCA analysis. POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.fam : A .fam file in plink format describing the 1,387 individuals used in the thinned dataset for the PCA analysis. affyProves-rsid.txt : A mapping of Affymetrix probe names to rsid's. POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.out0-PCA.par : Input file for smartpca POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.out0-PCA.eigs : Smartpca output with individual coordinates POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.out0-PCA.eval : Smartpca output with eigenvalues POPRES_08_24_01.EuroThinFinal.LD_0.8.exLD.out0-PCA.snpeigs : Smartpca output containing SNP loadings that define the principal components
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