gap: pgc – R documentation

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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. 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

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.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)

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

pgc