homozygote {GeneticsBase}R Documentation

Flag observations with specific allele patterns

Description

homozygote
Flag observatsions with identical alleles
heterozygote
Flag observations with discordant alleles
carrier
Flag observations containing a specified allele
dominant
Flag observations containing one or more of the specified alleles.
recessive
Flag observations containing only the specified alleles.

Usage

homozygote(object, ...)
homozygote.geneSet(object, allele.names, marker, ...)

heterozygote(object, ...)
heterozygote.geneSet(object, allele.names, marker, ...)

carrier(object, ...)
carrier.geneSet(object, allele.names, marker, ...)

dominant(object, ...)
dominant.geneSet(object, allele.names, marker, ...)

recessive(object, ...)
recessive.geneSet(object, allele.names, marker, ...)

Arguments

object geneSet object
allele.names (optional) allele names.
marker (optional) marker names
... (optional) additional arguments supplied

Value

matrix of logicals.

Author(s)

Gregory R. Warnes warnes@bst.rochester.edu and Nitin Jain nitin.jain@pfizer.com

See Also

geneSet, extractAlleles

Examples


data(CAMP)
lCAMP <- CAMP[,1:10] # 10 observations

# see the genotypes
genotypes(lCAMP)

# which ones are homozygotes?
homozygote(lCAMP)

# which ones are carriers  for allele "2"?
carrier(lCAMP, allele.names="2")

# which markers are heterozygotes for marker m709
heterozygote(lCAMP, marker="m709")

# if '1' is dominant, which ones will show the
# '1' phenotype for marker m47?
dominant(lCAMP, allele.names="1", marker="m47")

# if '2' is recessive, which ones will show the
# '2' phenotype for marker m523?
recessive(lCAMP, allele.names="2", marker="p523")


[Package GeneticsBase version 1.8.0 Index]