AGT: AGT data set

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

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.