| locus {genetics} | R Documentation |
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.
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)
as.character.locus(x, ...)
as.character.gene(x, ...)
as.character.marker(x, ...)
getlocus(x, ...)
locus(x) <- value
marker(x) <- value
gene(x) <- value
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 |
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. |
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. |
Gregory R. Warnes warnes@bst.rochester.edu
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)