gap: genecounting – R documentation

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gap

genecounting

Gene counting for haplotype analysis

Description

Gene counting for haplotype analysis with missing data

Usage

genecounting(data,weight=NULL,loci=NULL,control=gc.control())

Arguments

`data`	genotype table
`weight`	a column of frequency weights
`loci`	an array containing number of alleles at each locus
`control`	is a function with the following arguments: xdata. a flag indicating if the data involves X chromosome, if so, the first column of data indicates sex of each subject: 1=male, 2=female. The marker data are no different from the autosomal version for females, but for males, two copies of the single allele present at a given 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 tol. tolerance for genotype probabilities with default value 1e-8 maxit. maximum number of iterations, with default value 50 pl. criteria for trimming haplotypes according to posterior probabilities assignment. filename containing haplotype assignment verbose. If TRUE, yields print out from the C routine

Value

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

References

Zhao, J. H., Lissarrague, S., Essioux, L. and P. C. Sham (2002). GENECOUNTING: 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

Zhao, J. H. (2004). 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics, 20, 1325-1326

Note

adapted from GENECOUNTING

Author(s)

Jing Hua Zhao

Examples

## Not run: 
require(gap.datasets)
# HLA data
data(hla)
hla.gc <- genecounting(hla[,3:8])
summary(hla.gc)
hla.gc$l0
hla.gc$l1

# ALDH2 data
data(aldh2)
control <- gc.control(handle.miss=1,assignment="ALDH2.out")
aldh2.gc <- genecounting(aldh2[,3:6],control=control)
summary(aldh2.gc)
aldh2.gc$l0
aldh2.gc$l1

# Chromosome X data
# assuming allelic data have been extracted in columns 3-13
# and column 3 is sex
filespec <- system.file("tests/genecounting/mao.dat")
mao2 <- read.table(filespec)
dat <- mao2[,3:13]
loci <- c(12,9,6,5,3)
contr <- gc.control(xdata=TRUE,handle.miss=1)
mao.gc <- genecounting(dat,loci=loci,control=contr)
mao.gc$npusr
mao.gc$npdat

## End(Not run)

gap

Genetic Analysis Package

v1.2.3-1

GPL (>= 2)

Authors

Jing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley

Initial release

2021-4-21