ade4 (version 1.4-3)

hdpg: Genetic Variation In Human Populations

Description

This data set gives genotypes variation of 1066 individuals belonging to 52 predefined populations, for 404 microsatellite markers.

Usage

data(hdpg)

source

Extract of data prepared by the Human Diversity Panel Genotypes http://research.marshfieldclinic.org/genetics/Freq/FreqInfo.htm

prepared by Hinda Haned, from data used in: Noah A. Rosenberg, Jonatahan K. Pritchard, James L. Weber, Howard M. Cabb, Kenneth K. Kidds, Lev A. Zhivotovsky, Marcus W. Feldman (2002) Genetic Structure of human Populations Science, 298, 2381--2385.

Lev A. Zhivotovsky, Noah Rosenberg, and Marcus W. Feldman (2003). Features of Evolution and Expansion of Modern Humans, Inferred from Genomewide Microsatellite Markers Am. J. Hum. Genet, 72, 1171--1186.

Details

The rows of hdpg$pop are the names of the 52 populations belonging to the geographic regions contained in the rows of hdpg$region. The chosen regions are: America, Asia, Europe, Middle East North Africa, Oceania, Subsaharan AFRICA. The 52 populations are: Adygei, Balochi, Bantu, Basque, Bedouin, Bergamo, Biaka Pygmies, Brahui, Burusho, Cambodian, Columbian, Dai, Daur, Druze, French, Han, Hazara, Hezhen, Japanese, Kalash, Karitiana, Lahu, Makrani, Mandenka, Maya, Mbuti Pygmies, Melanesian, Miaozu, Mongola, Mozabite, Naxi, NewGuinea, Nilote, Orcadian, Oroqen, Palestinian, Pathan, Pima, Russian, San, Sardinian, She, Sindhi, Surui, Tu, Tujia, Tuscan, Uygur, Xibo, Yakut, Yizu, Yoruba. hdpg$freq is a data frame with 52 rows, corresponding to the 52 populations described above, and 4992 microsatellite markers.

Examples

library(ade4)
data(hdpg)
freq <- char2genet(hdpg$tab, hdpg$ind$population)
vec <- apply(freq$tab, 2, function(c) mean(c, na.rm = TRUE))
for (j in 1:4492){
    freq$tab[is.na(freq$tab[,j]),j] = vec[j]}
pcatot <- dudi.pca(freq$tab, center = TRUE, scale = FALSE, scannf = FALSE, nf = 4)
s.label(pcatot$li, xax = 1, yax = 2, sub = "1-2", lab = freq$pop.names)