Ravages (version 1.1.3)

LCT.matrix: 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)

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")]