adwave (version 1.1)

admix: Simulated Admixed Population Data

Description

The data set provides simulated allele calls for 50 individuals from 3 populations. We consider a simple admixture scenario where two ancestral populations, popA (sample size $n_A = 15$) and popB (sample size $n_B = 15$), merged 160 generations ago to form the admixed population, popAB (sample size $n_{AB} = 20$). The ancestral populations contributed to the admixed population with probability 0.5.

Usage

data(admix)

Format

List with the following entries

• data: 3,000 x 50 data matrix with 3,000 genotype calls (rows) versus 50 individuals (columns). Raw entries take the value 0 if heterozygous, and -1 or 1 if homozygous. SNPs are ordered by their physical positions. Column names list individual IDs, row names list SNP IDs.
• map: 3,000 x 2 data matrix providing mapping to genetic distance (‘recombination distance’) for each SNP.
• colplot: vector of length 50. Plotting color for each individual.
• populations: list of length 3. Character vectors giving the IDs of individuals in each population. IDs must map to the column names of the data matrix.

Details

Further description of the data can be found in Sanderson et al. (2015)

References

Sanderson, J., H. Sudoyo, T.M. Karafet, M.F. Hammer and M.P. Cox. 2015. Reconstructing past admixture processes from local genomic ancestry using wavelet transformation. Genetics 200:469-481.

Chen G.K., P. Marjoram and J.D. Wall. 2009. Fast and flexible simulation of DNA sequence data. Genome Research 19:136-142. doi:10.1101 gr.083634.108.

Examples

data(admix)
str(admix)