View source: R/rf_list_to_matrix.R
rf_list_to_matrix | R Documentation |
Transforms the recombination fraction list contained in an object
of class mappoly.twopt
or mappoly.twopt2
into a recombination
fraction matrix
rf_list_to_matrix(
input.twopt,
thresh.LOD.ph = 0,
thresh.LOD.rf = 0,
thresh.rf = 0.5,
ncpus = 1L,
shared.alleles = FALSE,
verbose = TRUE
)
## S3 method for class 'mappoly.rf.matrix'
print(x, ...)
## S3 method for class 'mappoly.rf.matrix'
plot(
x,
type = c("rf", "lod"),
ord = NULL,
rem = NULL,
main.text = NULL,
index = FALSE,
fact = 1,
...
)
input.twopt |
an object of class |
thresh.LOD.ph |
LOD score threshold for linkage phase configurations (default = 0) |
thresh.LOD.rf |
LOD score threshold for recombination fractions (default = 0) |
thresh.rf |
the threshold used for recombination fraction filtering (default = 0.5) |
ncpus |
number of parallel processes (i.e. cores) to spawn (default = 1) |
shared.alleles |
if |
verbose |
if |
x |
an object of class |
... |
currently ignored |
type |
type of matrix that should be printed. Can be one of the
following: |
ord |
the order in which the markers should be plotted (default = NULL) |
rem |
which markers should be removed from the heatmap (default = NULL) |
main.text |
a character string as the title of the heatmap (default = NULL) |
index |
|
fact |
positive integer. factor expressed as number of cells to be aggregated (default = 1, no aggregation) |
thresh_LOD_ph
should be set in order to only select
recombination fractions that have LOD scores associated to the
linkage phase configuration higher than thresh_LOD_ph
when compared to the second most likely linkage phase configuration.
A list containing two matrices. The first one contains the filtered recombination fraction and the second one contains the information matrix
Marcelo Mollinari, mmollin@ncsu.edu
Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/g3.119.400378")}
all.mrk <- make_seq_mappoly(hexafake, 1:20)
red.mrk <- elim_redundant(all.mrk)
unique.mrks <- make_seq_mappoly(red.mrk)
all.pairs <- est_pairwise_rf(input.seq = unique.mrks,
ncpus = 1,
verbose = TRUE)
## Full recombination fraction matrix
mat.full <- rf_list_to_matrix(input.twopt = all.pairs)
plot(mat.full)
plot(mat.full, type = "lod")
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