1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
|
\name{sim.map}
\alias{sim.map}
\title{Simulate a genetic map}
\description{
Simulate the positions of markers on a genetic map.
}
\usage{
sim.map(len=rep(100,20), n.mar=10, anchor.tel=TRUE,
include.x=TRUE, sex.sp=FALSE, eq.spacing=FALSE)
}
\arguments{
\item{len}{A vector specifying the chromosome lengths (in cM)}
\item{n.mar}{A vector specifying the number of markers per chromosome.}
\item{anchor.tel}{If true, markers at the two telomeres will always be
included, so if \code{n.mar} = 1 or 2, we'll give just the two
telomeric markers.}
\item{include.x}{Indicates whether the last chromosome should be
considered the X chromosome.}
\item{sex.sp}{Indicates whether to create sex-specific maps, in which
case the output will be a vector of 2-row matrices, with rows
corresponding to the maps for the two sexes.}
\item{eq.spacing}{If TRUE, markers will be equally spaced.}
}
\details{
Aside from the telomeric markers, marker positions are simulated as
iid Uniform(\eqn{0,L}). If \code{len} or \code{n.mar} has just one element,
it is expanded to the length of the other argument. If they both have
just one element, only one chromosome is simulated.
If \code{eq.spacing} is TRUE, markers are equally spaced between 0 and
\eqn{L}. If \code{anchor.tel} is FALSE, telomeric markers are not
included.
}
\value{
A list of vectors, each specifying the locations of the markers. Each
component of the list is given class \code{A} or \code{X}, according
to whether it is autosomal or the X chromosome.
}
\author{Karl W Broman, \email{broman@wisc.edu} }
\examples{
# simulate 4 autosomes, each with 10 markers
map <- sim.map(c(100,90,80,40), 10, include.x=FALSE)
plotMap(map)
# equally spaced markers
map2 <- sim.map(c(100,90,80,40), 10, include.x=FALSE, eq.spacing=TRUE)
plot(map2)
}
\seealso{ \code{\link{sim.cross}}, \code{\link{plotMap}},
\code{\link{replace.map}}, \code{\link{pull.map}} }
\keyword{datagen}
|
