locus: Creates an object of class "locus"

View source: R/locus.q

locusR Documentation

Creates an object of class "locus"

Description

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

Usage

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

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 Nov. 29, 2022, 1:06 a.m.