admix: Simulated Admixed Population Data

In adwave: Wavelet Analysis of Genomic Data from Admixed Populations

Description

The example dataset 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

A list with the following entries:

• data: 3,000 x 50 data matrix with 3,000 genotype calls (rows) for 50 individuals (columns). Raw entries take the value 0 if heterozygous, and -1 or 1 if homozygous. Polymorphisms are ordered by their physical positions. Column names list individual IDs, row names list polymorphism IDs.

• map: 3,000 x 2 data matrix providing a mapping to genetic distance (‘recombination distance’) for each polymorphism.

• 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 dataset can be found in Sanderson et al. (2015). The data were simulated using MaCS (Chen et al. 2009).

References

Sanderson J, H Sudoyo, TM Karafet, MF Hammer and MP Cox. 2015. Reconstructing past admixture processes from local genomic ancestry using wavelet transformation. Genetics 200:469-481. https://doi.org/10.1534/genetics.115.176842

Chen GK, P Marjoram and JD Wall. 2009. Fast and flexible simulation of DNA sequence data. Genome Research 19:136-142. https://doi.org/10.1101/gr.083634.108

Examples

data(admix)
str(admix) 

Example output

Loading required package: waveslim

waveslim: Wavelet Method for 1/2/3D Signals (version = 1.7.5.1)

List of 4
 $ data       : num [1:3000, 1:50] 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:3000] "8574" "22507" "45946" "86114" ...
  .. ..$ : chr [1:50] "P100001" "P100002" "P100003" "P100004" ...
 $ map        : num [1:3000, 1:2] 8574 22507 45946 86114 107144 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:2] "PhysPos" "GenMap"
 $ colplot    : num [1:50] 3 3 3 3 3 3 3 3 3 3 ...
 $ populations:List of 3
  ..$ popA : chr [1:15] "P100001" "P100002" "P100003" "P100004" ...
  ..$ popB : chr [1:15] "P200001" "P200002" "P200003" "P200004" ...
  ..$ popAB: chr [1:20] "AD00001" "AD00002" "AD00003" "AD00004" ...

adwave documentation built on May 1, 2019, 8 p.m.