haplosim {hapsim} | R Documentation |
Generates a random sample of haplotypes, given an haplotype object created from a data set.
haplosim(n, hap, which.snp = NULL, seed = NULL, force.polym = TRUE)
n |
Number of haplotypes to generate |
hap |
Haplotype object created with haplodata |
which.snp |
A vector specifying which SNPs to include |
seed |
Seed for the random number generator |
force.polym |
if TRUE, all loci are polymorphic |
A list containing:
data |
Simulated sample |
freqs |
Allele frequency vector |
cor |
Correlation matrix |
div |
Locus-specific diversity scores |
mse.freqs |
MSE of allele frequencies |
mse.cor |
MSE of correlations |
Giovanni Montana
Montana, G. HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients. 2005.
See also haplodata
data(ACEdata) # create the haplotype object x <- haplodata(ACEdata) # simulates a first sample of 100 haplotypes using all markers y1 <- haplosim(100, x) # compares allele frequencies in real and simulated samples plot(x$freqs, y1$freqs, title=paste("MSE:",y1$mse.freqs)); abline(a=0, b=1) # compares LD coefficients in real and simulated samples ldplot(mergemats(x$cor, y1$cor), ld.type='r') # simulates a second sample of 1000 haplotypes using the first 20 markers only y2 <- haplosim(1000, which.snp=seq(20), x)