gap (version 0.8-2)

pgc: 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

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

See Also

genecounting

Examples

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)