genecounting {gap} | R Documentation |
Gene counting for haplotype analysis with missing data
genecounting(data,weight=NULL,loci=NULL,convll=1,handle.miss=0,eps=0.00001,maxit=50,pl=0.001)
data |
genotype table |
weight |
a column of frequency weights |
loci |
an array containing number of alleles at each locus |
convll |
set convergence criteria according to log-likelihood, if its value set to 1 |
handle.miss |
to handle missing data, if its value set to 1 |
eps |
the actual convergence criteria, with default value 1e-5 |
maxit |
maximum number of iterations, with default value 50 |
pl |
criteria for trimming haplotypes according to posterior probabilities |
The returned value is a list containing:
h |
haplotype frequency estimates under linkage disequilibrium (LD) |
h0 |
haplotype frequency estimates under linkage equilibrium (no LD) |
prob |
genotype probability estimates |
l0 |
log-likelihood under linkage equilibrium |
l1 |
log-likelihood under linkage disequilibrium |
hapid |
unique haplotype identifier (defunct, see gc.em) |
npusr |
number of parameters according user-given alleles |
npdat |
number of parameters according to observed |
htrtable |
design matrix for haplotype trend regression (defunct, see gc.em) |
iter |
number of iterations used in gene counting |
converge |
a flag indicating convergence status of gene counting |
di0 |
haplotype diversity under no LD, defined as 1-sum (h0^2) |
di1 |
haplotype diversity under LD, defined as 1-sum (h^2) |
resid |
residuals in terms of frequency weights = o - e |
Zhao, J. H., Lissarrague, S., Essioux, L. and P. C. Sham (2002). Gene-counting for haplotype analysis with missing genotypes. Bioinformatics 18(12):1694-1695
Zhao, J. H. and P. C. Sham (2003). Generic number systems and haplotype analysis. Comp Meth Prog Biomed 70: 1-9
adapted from GENECOUNTING
Jing hua Zhao
## Not run: # Now we use the HLA data for testing data(hla) hla.gc<-genecounting(hla[,3:8]) summary(hla.gc) hla.gc$l0 hla.gc$l1 # Now we use ALDH2 data data(aldh2) aldh2.gc<-genecounting(aldh2[,3:6],handle.miss=1) summary(aldh2.gc) aldh2.gc$l0 aldh2.gc$l1 ## End(Not run)