gc.em | R Documentation |
Gene counting for haplotype analysis
gc.em(
data,
locus.label = NA,
converge.eps = 1e-06,
maxiter = 500,
handle.miss = 0,
miss.val = 0,
control = gc.control()
)
data |
Matrix of alleles, such that each locus has a pair of adjacent columns of alleles, and the order of columns corresponds to the order of loci on a chromosome. If there are K loci, then ncol(data) = 2*K. Rows represent alleles for each subject. |
locus.label |
Vector of labels for loci, of length K (see definition of data matrix). |
converge.eps |
Convergence criterion, based on absolute change in log likelihood (lnlike). |
maxiter |
Maximum number of iterations of EM. |
handle.miss |
a flag for handling missing genotype data, 0=no, 1=yes. |
miss.val |
missing value. |
control |
a function, see genecounting. |
Gene counting for haplotype analysis with missing data, adapted for hap.score
List with components:
converge Indicator of convergence of the EM algorithm (1=converged, 0 = failed).
niter Number of iterations completed in the EM alogrithm.
locus.info A list with a component for each locus. Each component is also a list, and the items of a locus- specific list are the locus name and a vector for the unique alleles for the locus.
locus.label Vector of labels for loci, of length K (see definition of input values).
haplotype Matrix of unique haplotypes. Each row represents a unique haplotype, and the number of columns is the number of loci.
hap.prob Vector of mle's of haplotype probabilities. The ith element of hap.prob corresponds to the ith row of haplotype.
hap.prob.noLD Similar to hap.prob, but assuming no linkage disequilibrium.
lnlike Value of lnlike at last EM iteration (maximum lnlike if converged).
lr Likelihood ratio statistic to test no linkage disequilibrium among all loci.
indx.subj Vector for index of subjects, after expanding to all possible pairs of haplotypes for each person. If indx=i, then i is the ith row of input matrix data. If the ith subject has n possible pairs of haplotypes that correspond to their marker phenotype, then i is repeated n times.
nreps Vector for the count of haplotype pairs that map to each subject's marker genotypes.
hap1code Vector of codes for each subject's first haplotype. The values in hap1code are the row numbers of the unique haplotypes in the returned matrix haplotype.
hap2code Similar to hap1code, but for each subject's second haplotype.
post Vector of posterior probabilities of pairs of haplotypes for a person, given thier marker phenotypes.
htrtable A table which can be used in haplotype trend regression.
Adapted from GENECOUNTING.
Jing Hua Zhao
zhao02gap
\insertRefzhao03gap
genecounting
, LDkl
## Not run:
data(hla)
gc.em(hla[,3:8],locus.label=c("DQR","DQA","DQB"),control=gc.control(assignment="t"))
## End(Not run)
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