pgc {gap}R Documentation

Preparing weight for GENECOUNTING

Description

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.

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

References

Zhao JH, Sham PC (2003). Generic number system and haplotype analysis. Comp Prog Meth Biomed 70:1-9

Note

Built on pgc.c

Author(s)

Jing Hua Zhao

See Also

genecounting,hwe.hardy

Examples

## Not run: 

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.miss=0)

# 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)

[Package gap version 1.0-17 Index]