haplo.em.w {GeneticsBase}R Documentation

Wrapper for EM computation of haplotype probabilities, with Progressive Insertion

Description

Wrapper for EM computation of haplotype probabilities, with Progressive Insertion.

Usage

haplo.em.w(geneSetObj, 
           locus.label = NA, 
           miss.val = c(0, NA), 
           weight = NULL, 
           control = haplo.em.control())

Arguments

geneSetObj a geneSet object.
locus.label vector of labels for loci.
miss.val vector of values that represent missing alleles in geno.
weight weights for observations.
control list of control parameters. The default is constructed by the function haplo.em.control.

Details

Please refer to haplo.em for more details.

Value

list with components:

converge indicator of convergence of the EM algorithm (1 = converge, 0 = failed).
lnlike value of lnlike at last EM iteration (maximum lnlike if converged).
lr likelihood ratio statistic to test the final lnlike against the lnlike that assumes complete linkage equilibrium among all loci (i.e., haplotype frequencies are products of allele frequencies).
df.lr degrees of freedom for likelihood ratio statistic. The df for the unconstrained final model is the number of non-zero haplotype frequencies minus 1, and the df for the null model of complete linkage equilibrium is the sum, over all loci, of (number of alleles - 1). The df for the lr statistic is df[unconstrained] - df[null]. This can result in negative df, if many haplotypes are estimated to have zero frequency, or if a large amount of trimming occurs, when using large values of min.posterior in the list of control parameters.
hap.prob vector of mle's of haplotype probabilities. The ith element of hap.prob corresponds to the ith row of haplotype.
locus.label vector of labels for loci, of length K (see definition of input values).
subj.id vector of id's for subjects used in the analysis, based on row number of input geno matrix. If subjects are removed, then their id will be missing from subj.id.
rows.rem now defunct, but set equal to a vector of length 0, to be compatible with other functions that check for rows.rem.
indx.subj vector for row index of subjects after expanding to all possible pairs of haplotypes for each person. If indx.subj=i, then i is the ith row of geno. If the ith subject has n possible pairs of haplotypes that correspond to their marker genotype, then i is repeated n times.
nreps vector for the count of haplotype pairs that map to each subject's marker genotypes.
max.pairs vector of maximum number of pairs of haplotypes per subject that are consistent with their marker data in the matrix geno. The length of max.pairs = nrow(geno). This vector is computed by geno.count.pairs.
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 their marker phenotypes.
haplotype matrix of unique haplotypes. Each row represents a unique haplotype, and the number of columns is the number of loci.
control list of control parameters for algorithm. See haplo.em.control

Note

~~further notes~~

Author(s)

Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu

References

~put references to the literature/web site here ~

See Also

haplo.scan.w, haplo.score.slide.w, haplo.score.w

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--    or do  help(data=index)  for the standard data sets.

## The function is currently defined as
"haplo.em.w"

[Package GeneticsBase version 1.2.0 Index]