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LCT

LCT data set

Description

These data have been extracted from the 1000 Genomes data. The data set contains the genotype matrix LCT.gen, the pedigree matrix LCT.fam and a matrix LCT.bim, corresponding to 503 individuals of European populations and 607 SNPs on chromosome 2, on a ~300kb segment containing the Lactase gene. There is also a factor LCT.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).

Note that the SNP rs4988235 is associated with lactase persistence / lactose intolerence.

Usage

data(LCT)

Format

There are three data objects in the dataset:

LCT.gen: Genotype matrix
LCT.fam: Data frame containing all variables corresponding to a .fam file
LCT.bim: Data frame containing all variables corresponding to a .bim file
LCT.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(LCT)
x <- as.bed.matrix(LCT.gen, LCT.fam, LCT.bim)
x
which(x@snps$id == "rs4988235")

gaston

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

v1.5.7

GPL-3

Authors

Hervé Perdry [cre, aut, cph], Claire Dandine-Roulland [aut, cph], Deepak Bandyopadhyay [cph] (C++ gzstream class), Lutz Kettner [cph] (C++ gzstream class)

Initial release

2020-09-18

LCT