haplo.em.w {GeneticsBase} | R Documentation |
Wrapper for EM computation of haplotype probabilities, with Progressive Insertion.
haplo.em.w(geneSetObj, locus.label = NA, miss.val = c(0, NA), weight = NULL, control = haplo.em.control())
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 . |
Please refer to haplo.em
for more details.
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 |
~~further notes~~
Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu
~put references to the literature/web site here ~
haplo.scan.w
, haplo.score.slide.w
, haplo.score.w
##---- 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"