The CEU-CHD-YRI admixed simulation data

Description

The list data has five compoents: admixed, anc1, anc2, anc3, true.local.ancestry, position. The data matrixes were simulated data using the allele frequencies from HapMap Population CEU (Utah residents with Northern and Western European ancestry from the CEPH collection), CHD (Chinese in Metropolitan Denver, Colorado), and YRI (Yoruba in Ibadan, Nigeria (West Africa)).

Usage

ceuchdyri

Format

A list consisting of admixed (10000 rows, 30 columns), anc1 (10000 rows, 60 columns), anc2 (10000 rows, 60 columns), anc3 (10000 rows and 60 columns), true.local.ancestry (10000 rows, 60 columns), and position (a vector of length 10000).

The elements of the matrixes (admixed, anc1, anc2, anc3) are the genotypes being coded as the number of copies of the variant allele present, 0, 1 or 2. The elements of matrix true.local.ancestry are the true local ancestries being coded as alleles identification from ancestries 1, 2, or 3. The physical positions (in base pairs unit) are in position.

Source

none

References

Yang, J. J., LI, J., Buu, A., and Williams, L. K. (2013) Efficient Inference of Local Ancestry. Bioinformatics. doi: 10.1093/bioinformatics/btt488

Examples

  data(ceuchdyri)
  str(ceuchdyri)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(EILA)
Loading required package: class
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/EILA/ceuchdyri.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ceuchdyri
> ### Title: The CEU-CHD-YRI admixed simulation data
> ### Aliases: ceuchdyri
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   data(ceuchdyri)
>   str(ceuchdyri)
List of 6
 $ anc1               : num [1:10000, 1:60] 0 1 0 2 2 2 2 2 2 0 ...
 $ anc2               : num [1:10000, 1:60] 0 0 0 2 2 2 2 2 2 1 ...
 $ anc3               : num [1:10000, 1:60] 0 0 1 1 0 2 0 2 0 2 ...
 $ admixed            : num [1:10000, 1:30] 0 0 0 2 2 2 2 2 2 1 ...
 $ true.local.ancestry: num [1:10000, 1:30] 22 22 22 22 22 22 22 22 22 22 ...
 $ position           : int [1:10000] 554340 711153 730720 742429 775852 878522 908436 916294 936897 980280 ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>