locus: Creates an object of class "locus"

Description Usage Arguments Value Examples

View source: R/locus.q

Description

Creates an object containing genotypes for multiple individuals. The object can then use method functions developed for objects of class "locus".

Usage

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locus(allele1, allele2, chrom.label=NULL,locus.alias=NULL,
     x.linked=FALSE, sex=NULL, male.code="M", female.code="F", miss.val=NA)

Arguments

allele1

A vector containing the labels for 1 allele for a set of individuals, or optionally a matrix with 2 columns each containing an allele for each person.

allele2

A vector containing the labels for the second allele for a set of individuals. If allele 1 is a matrix, allele 2 need not be specified.

chrom.label

A label describing the chromosome the alleles belong to

locus.alias

A vector containing one or more aliases describing the locus. The first alias in the vector will be used as a label for printing in some functions such as multilocus.print().

x.linked

A logical value denoting whether the chromosome is x linked

sex

A vector containing the gender of each individual (required if x.linked=T)

male.code

The code denoting a male in the sex vector

female.code

The code denoting a female in the sex vector

miss.val

a vector of codes denoting missing values for allele1 and allele2. Note that NA will always be treated as a missing value, even if not specified in miss.val. Also note that if multiple missing value codes are specified, the original missing value code for a specific individual can not be retrieved from the locus object.

Value

Returns an object of class locus which inherits from class model.matrix containing the following elements:

geno

a matrix with 2 columns where each row contains numeric codes for the 2 alleles for an individual.

chrom.label

a chromosome label

locus.alias

a vector of aliases for the locus

x.linked

a logical value specifying if the locus is x-linked or not

allele.labels

a vector of labels corresponding to the numeric codes in matrix geno (similar to levels in a factor)

male.code

a code to be used to identify males for an x.linked locus.

female.code

a code to be used to identify females for an x.linked locus.

Examples

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b1 <- c("A","A","B","C","E","D")
b2 <- c("A","A","C","E","F","G")
loc1 <- locus(b1,b2,chrom=4,locus.alias="D4S1111")

loc1

# a second example which uses more parameters, some may not be supported.
c1 <- c(101,10, 112,112,21,112)
c2 <- c(101,101,112,  100,21, 10)

gender <- rep(c("M","F"),3)
loc2 <- locus(c1,c2,chrom="X",locus.alias="DXS1234", x.linked=TRUE, sex=gender)

loc2

haplo.stats documentation built on Sept. 5, 2021, 5:36 p.m.