genetics: locus – R documentation

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locus

Create and Manipulate Locus, Gene, and Marker Objects

Description

locus, gene, and marker create objects to store information, respectively, about genetic loci, genes, and markers.

is.locus, is.gene, and ismarker test whether an object is a member of the respective class.

as.character.locus, as.character.gene, as.character.marker return a character string containing a compact encoding the object.

getlocus, getgene, getmarker extract locus data (if present) from another object.

locus<-, marker<-, and gene<- adds locus data to an object.

Usage

locus(name, chromosome, arm=c("p", "q", "long", "short", NA),
        index.start, index.end=NULL)

  gene(name, chromosome, arm=c("p", "q", "long", "short"),
       index.start, index.end=NULL)

  marker(name, type, locus.name, bp.start, bp.end = NULL,
         relative.to = NULL, ...)

  is.locus(x)

  is.gene(x)

  is.marker(x)

  ## S3 method for class 'locus'
as.character(x, ...)

  ## S3 method for class 'gene'
as.character(x, ...)

  ## S3 method for class 'marker'
as.character(x, ...)

  getlocus(x, ...)

  locus(x) <- value

  marker(x) <- value

  gene(x) <- value

Arguments

`name`	character string giving locus, gene, or marker name
`chromosome`	integer specifying chromosome number (1:23 for humans).
`arm`	character indicating long or short arm of the chromosome. Long is be specified by "long" or "p". Short is specified by "short" or "q".
`index.start`	integer specifying location of start of locus or gene on the chromosome.
`index.end`	optional integer specifying location of end of locus or gene on the chromosome.
`type`	character string indicating marker type, e.g. "SNP"
`locus.name`	either a character string giving the name of the locus or gene (other details may be specified using `...`) or a `locus` or `gene` object.
`bp.start`	start location of marker, in base pairs
`bp.end`	end location of marker, in base pairs (optional)
`relative.to`	location (optional) from which `bp.start` and `bp.end` are calculated.
`...`	parameters for `locus` used to fill in additional details on the locus or gene within which the marker is located.
`x`	an object of class `locus`, `gene`, or `marker`, or (for `getlocus`, `locus<-`, `marker<-`, and `gene<-`) an object that may contain a locus attribute or field, notably a `genotype` object.
`value`	`locus`, `marker`, or `gene` object

Value

Object of class locus and geneare lists with the elements:

`name`	character string giving locus, gene, or marker name
`chromosome`	integer specifying chromosome number (1:23 for humans).
`arm`	character indicating long or short arm of the chromosome. Long is be specified by "long" or "p". Short is specified by "short" or "q".
`index.start`	integer specifying location of start of locus or gene on the chromosome.
`index.end`	optional integer specifying location of end of locus or gene on the chromosome.

Objects of class marker add the additional fields:

`marker.name`	character string giving the name of the marker
`bp.start`	start location of marker, in base pairs
`bp.end`	end location of marker, in base pairs (optional)
`relative.to`	location (optional) from which `bp.start` and `bp.end` are calculated.

Author(s)

Gregory R. Warnes greg@warnes.net

Examples

ar2  <- gene("AR2",chromosome=7,arm="q",index.start=35)
ar2

par  <- locus(name="AR2 Psedogene",
              chromosome=1,
              arm="q",
              index.start=32,
              index.end=42)
par

c109t  <- marker(name="C-109T",
                 type="SNP",
                 locus.name="AR2",
                 chromosome=7,
                 arm="q",
                 index.start=35,
                 bp.start=-109,
                 relative.to="start of coding region")
c109t

c109t  <- marker(name="C-109T",
                 type="SNP",
                 locus=ar2,
                 bp.start=-109,
                 relative.to="start of coding region")
c109t




example.data   <- c("D/D","D/I","D/D","I/I","D/D",
                    "D/D","D/D","D/D","I/I","")
g1  <- genotype(example.data, locus=ar2)
g1

getlocus(g1)

summary(g1)
HWE.test(g1)

g2  <- genotype(example.data, locus=c109t)
summary(g2)

getlocus(g2)

heterozygote(g2)
homozygote(g1)

allele(g1,1)

carrier(g1,"I")

heterozygote(g2)

genetics

Population Genetics

v1.3.8.1.3

GPL

Authors

Gregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch, and Michael Man.

Initial release

2012-11-26