LCT.matrix: LCT genotypes matrix

In Ravages: Rare Variant Analysis and Genetic Simulations

LCT genotypes matrix

Description

These data contain the genotype matrix corresponding to haplotypes present in LCT.haplotypes from the 1000 Genomes data for a ~300kb segment containing the Lactase gene. Information about individuals is present in LCT.matrix.fam, and information about population (population and super population) is present in LCT.matrix.pop1000G, in a format needed to generate a bedmatrix. LCT.snps from LCT.haplotypes can be used as the corresponding bim file of this genotypes matrix.

Usage

 data(LCT.matrix) 

Format

Three data objects are present in LCT.haplotypes:

LCT.matrix.bed

The matrix of genotypes

LCT.matrix.fam

The corresponding fam file

LCT.matrix.pop1000G

A data frame with population information for individuals (population, superpopulation)

Source

Data were obtained from the 1000 Genomes Project.

References

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

See Also

LCT.haplotypes

Examples

#Import data in a bed matrix
x <- as.bed.matrix(x=LCT.matrix.bed, fam=LCT.matrix.fam, bim=LCT.snps)
#Add population
x@ped[,c("pop", "superpop")] <- LCT.matrix.pop1000G[,c("population", "super.population")]

Ravages documentation built on April 1, 2023, 12:08 a.m.