map {onemap} | R Documentation |
Does soma data manipulation and calls rcd
to
order genetic markers on a linkage group (object of class5
extracted.group
).
map(w, y, LOD = NULL, max.rf = NULL) ## S3 method for class 'map': print(x, cumulative=FALSE, ...)
w |
an object of class extracted group (the group to be
ordered). |
y |
the object of class rf.2pts that was used to generate
object w , i.e., that contains the results of two-point
analyses. |
LOD |
minimum LOD Score to declare linkage. If NULL
(default) the threshold already present in object y is used. |
max.rf |
maximum recombination fraction to declare linkage. If
NULL (default) the threshold already present in object
y is used. |
x |
an object of class map . |
cumulative |
logical. If FALSE (default), distances
between markers are printed independently for each interval. If
TRUE , cumulative distances are displayed (for compatibility
purposes with softwares used to draw chromosomes). |
... |
further arguments, passed to other methods. Currently ignored. |
An object of class map
, which is a list with the following
components:
order |
a numeric vector with the estimated order of genetic markers. |
recomb |
a (symmetric) matrix with two-point estimates of the recombination fraction between markers, for all pairs of markers in the linkage group, under the most probable assignment for each pair. |
marnames |
names of markers present in the linkage group, according to the original input file. |
number |
number of the linkage group, according to the numeration
in the object of class group from where the linkage group was
extracted. |
name |
name of the object of class group from where the
linkage group was extracted. |
LOD |
minimum LOD Score to declare linkage. |
max.rf |
maximum recombination fraction to declare linkage. |
phases |
a (symmetric) matrix with the most probable linkage phase (assignment) between markers, for each pair of markers in the linkage group. |
Currently only Rapid Chain Delineation is available (Doerge, 1996). Other ordering algorithms will be made available soon.
Gabriel R A Margarido, gramarga@esalq.usp.br
Doerge, R. W. (1996) Constructing genetic maps by rapid chain delineation. Journal of Quantitative Trait Loci 2: 121-132.
Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.
group
, extract.group
,
rcd
, make.map
data(example_out) twopts <- est.rf.2pts(example_out) link_gr <- group(twopts) LG1 <- extract.group(link_gr,1) LG1_map <- map(LG1,twopts) # order makers LG1_map