R: Creates an object of class "locus"

locus {haplo.stats} | R 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

[Package haplo.stats version 1.7.9 Index]