pgc {gap}

Preparing weight for GENECOUNTING

Description

Preparing weight for GENECOUNTING

Usage

pgc(data, handle.miss = 1, is.genotype = 0, with.id = 0)

Arguments

data

the multilocus genotype data for a set of individuals.

handle.miss

a flag to indicate if missing data is kept, 0 = no, 1 = yes.

is.genotype

a flag to indicate if the data is already in the form of genotype identifiers.

with.id

a flag to indicate if the unique multilocus genotype identifier is generated.

Details

This function is a R port of the GENECOUNTING/PREPARE program which takes an array of genotyep data and collapses individuals with the same multilocus genotype. This function can also be used to prepare for the genotype table in testing Hardy-Weinberg equilibrium.

Value

The returned value is a list containing:

• cdata the collapsed genotype data.

• wt the frequency weight.

• obscom the observed number of combinations or genotypes.

• idsave optional, available only if with.id = 1.

Note

Built on pgc.c.

Author(s)

Jing Hua Zhao

References

Zhao JH, Sham PC (2003). “Generic number systems and haplotype analysis.” Comput Methods Programs Biomed, 70(1), 1-9. ISSN 0169-2607 (Print) 0169-2607, doi:10.1016/s0169-2607(01)00193-6.

See Also

genecounting, hwe.hardy

Examples

## Not run: 
require(gap.datasets)
data(hla)
x <- hla[,3:8]

# do not handle missing data
y<-pgc(x,handle.miss=0,with.id=1)
hla.gc<-genecounting(y$cdata,y$wt)

# handle missing but with multilocus genotype identifier
pgc(x,handle.miss=1,with.id=1)

# handle missing data with no identifier
pgc(x,handle.miss=1,with.id=0)

## End(Not run)