Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/record.parallel.rfc.R
Implements the marker ordering algorithm Recombination Counting and Ordering (Van Os et al., 2005).
1 2 | record.parallel(input.seq, times = 10, cores = 1, LOD = 0, max.rf = 0.5,
tol = 1e-04, useC = TRUE)
|
input.seq |
an object of class |
times |
integer. Number of replicates of the RECORD procedure. |
cores |
Number of parallel processes. |
LOD |
minimum LOD-Score threshold used when constructing the pairwise recombination fraction matrix. |
max.rf |
maximum recombination fraction threshold used as the LOD value above. |
tol |
tolerance for the C routine, i.e., the value used to evaluate convergence. |
useC |
Use the C implementation to get the matrix of recombination fractions. |
Recombination Counting and Ordering (RECORD) is an algorithm
for marker ordering in linkage groups. It is not an exhaustive search
method and, therefore, is not computationally intensive. However, it does
not guarantee that the best order is always found. The only requirement is
a matrix with recombination fractions between markers. This implementation
parallelizes over the times
argument using cores
parallel
processes. An optimal choice for the cores
argument is usually an even
divisor of times
.
An object of class sequence
, which is a list containing the
following components:
seq.num |
a |
seq.phases |
a |
seq.rf |
a |
seq.like |
log-likelihood of the corresponding linkage map. |
data.name |
name of the object of class |
twopt |
name of the object of class |
Original implementation: Marcelo Mollinari, mmollina@usp.br, Parallel version: Bastian Schiffthaler, bastian.schiffthaler@umu.se
Mollinari, M., Margarido, G. R. A., Vencovsky, R. and Garcia, A. A. F. (2009) Evaluation of algorithms used to order markers on genetics maps. Heredity 103: 494-502.
Van Os, H., Stam, P., Visser, R.G.F. and Van Eck, H.J. (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theoretical and Applied Genetics 112: 30-40.
1 2 3 4 5 6 7 8 9 10 | ## Not run:
##outcross example
data(example.out)
twopt <- rf.2pts(example.out)
all.mark <- make.seq(twopt,"all")
groups <- group(all.mark)
LG1 <- make.seq(groups,1)
LG1.rec <- record(LG1)
## End(Not run)
|
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