AGT: AGT data set

AGTR Documentation

AGT data set

Description

These data have been extracted from the 1000 Genomes data. The data set contains the genotype matrix AGT.gen, the pedigree matrix AGT.fam and a matrix AGT.bim, corresponding to 503 individuals of European populations and 361 SNPs on chromosome 1, on a ~100kb segment containing the Angiotensinogen gene. There is also a factor AGT.pop, which gives the population from which each individual is drawn (CEU = Utah residents of Northern Western European ancestry, FIN = Finnish, GBR = England and Scottland, IBS = Iberian, TSI = Toscani).

Usage

 data(AGT) 

Format

There are three data objects in the dataset:

AGT.gen

Genotype matrix

AGT.fam

Data frame containing all variables corresponding to a .fam file

AGT.bim

Data frame containing all variables corresponding to a .bim file

AGT.pop

Factor giving the population from which each individual is drawn

Source

The data were obtained from the 1000 Genomes project (see https://www.internationalgenome.org/).

References

McVean et al, 2012, An integrated map of genetic variation from 1,092 human genomes, Nature 491, 56-65 doi:10.1038/nature11632

Examples

data(AGT)
x <- as.bed.matrix(AGT.gen, AGT.fam, AGT.bim)
x

gaston documentation built on May 29, 2024, 7:33 a.m.