| tryallpositions {qtl} | R Documentation |
Try all possible positions for a marker, keeping all other markers fixed, and evaluate the log likelihood and estimate the chromosome length.
tryallpositions(cross, marker, chr, error.prob=0.0001,
map.function=c("haldane","kosambi","c-f","morgan"),
m=0, p=0, maxit=4000, tol=1e-6, sex.sp=TRUE,
verbose=TRUE)
cross |
An object of class cross. See
read.cross for details. |
marker |
Character string with name of the marker to move about. |
chr |
A vector specifying which chromosomes to test for the
position of the marker. This should be a vector of character
strings referring to chromosomes by name; numeric values are
converted to strings. Refer to chromosomes with a preceding -
to have all chromosomes but those considered. A logical (TRUE/FALSE)
vector may also be used. |
error.prob |
Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype). |
map.function |
Indicates whether to use the Haldane, Kosambi, Carter-Falconer, or Morgan map function when converting genetic distances into recombination fractions. (Ignored if m > 0.) |
m |
Interference parameter for the chi-square model for interference; a non-negative integer, with m=0 corresponding to no interference. This may be used only for a backcross or intercross. |
p |
Proportion of chiasmata from the NI mechanism, in the Stahl model; p=0 gives a pure chi-square model. This may be used only for a backcross or intercross. |
maxit |
Maximum number of EM iterations to perform. |
tol |
Tolerance for determining convergence. |
sex.sp |
Indicates whether to estimate sex-specific maps; this is used only for the 4-way cross. |
verbose |
If TRUE, print information on progress. |
A data.frame with each row being a possible position for the marker.
The first two columns are the chromosome ID and position. The third
column is a LOD score comparing the hypotheses that the marker in that
position versus the hypothesis that it is not linked to that chromosome.
In the case of a 4-way cross, with sex.sp=TRUE, there are two
additional columns with the estimated female and male genetic lengths
of the respective chromosome, when the marker is in that position.
With sex.sp=FALSE, or for other types of crosses, there is one
additional column, with the estimated genetic length of the respective
chromosome, when the marker is in that position.
A final column contains a character string indicating the nearest
flanking markers for each interval.
Karl W Broman, kbroman@biostat.wisc.edu
est.map, ripple,
est.rf, switch.order,
movemarker
data(fake.bc) tryallpositions(fake.bc, "D7M301", 7, error.prob=0, verbose=FALSE)