locus: Create and Manipulate Locus, Gene, and Marker Objects

In kindlychung/genetics: Population Genetics

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 [e-mail]

See Also

genotype,

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)

kindlychung/genetics documentation built on May 20, 2019, 9:58 a.m.