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.

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.

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.

Note

Built on pgc.c.

References

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

Author

Jing Hua Zhao

Examples

if (FALSE) { # \dontrun{
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)
} # }