Get a list of objects for haplotype pairs
Get a list of objects for modeling haplotype pairs from a set of unique haplotypes and their frequencies, given the baseline haplotype
get.hapPair(haplo, haplo.freq, base.index)
haplo |
matrix of haplotypes, with rows the different haplotypes and columns the alleles of the haplotypes. For H haplotypes of L loci, haplo has dimension H x L. |
haplo.freq |
vector of length H for the population haplotype frequencies (corresponding to the rows of haplo) |
base.index |
integer index of the haplotype considered to be the base-line for logistic regression (index between 1 and H); often, the most common haplotype is chosen for the base-line. |
list with components:
p.g |
Genotype probability under Hardy-Weinberg Equilibrium, where the genotype is the haplotype pair |
x.haplo |
Design matrix for all pairs of haplotypes, excluding the baseline haplotype. Effects are coded to an additive effect for the haplotypes. |
haplo.indx |
two-column matrix containing the indices for the haplotypes in x.haplo. The indices are the row of the haplotype in haplo. |
haplo <- rbind(
c( 1, 2, 2, 1, 2),
c( 1, 2, 2, 1, 1),
c( 1, 1, 2, 1, 1),
c( 1, 2, 1, 1, 2),
c( 1, 2, 2, 2, 1),
c( 1, 2, 1, 1, 1),
c( 1, 1, 2, 2, 1),
c( 1, 1, 1, 1, 2),
c( 1, 2, 1, 2, 1),
c( 1, 1, 1, 2, 1),
c( 2, 2, 1, 1, 2),
c( 1, 1, 2, 1, 2),
c( 1, 1, 2, 2, 2),
c( 1, 2, 2, 2, 2),
c( 2, 2, 2, 1, 2),
c( 1, 1, 1, 1, 1),
c( 2, 1, 1, 1, 1),
c( 2, 1, 2, 1, 1),
c( 2, 2, 1, 1, 1),
c( 2, 2, 1, 2, 1),
c( 2, 2, 2, 1, 1))
dimnames(haplo)[[2]] <- paste("loc", 1:ncol(haplo), sep=".")
haplo <- data.frame(haplo)
haplo.freq <- c(0.170020121, 0.162977867, 0.123742455, 0.117706237, 0.097585513, 0.084507042,
0.045271630, 0.039235412, 0.032193159, 0.019114688, 0.019114688, 0.013078471,
0.013078471, 0.013078471, 0.013078471, 0.006036217, 0.006036217, 0.006036217,
0.006036217, 0.006036217, 0.006036217)
hPair <- get.hapPair(haplo, haplo.freq, base.index=1)
names(hPair)
dim(hPair$x.haplo)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.