est_rf_hmm | R Documentation |
Performs the multipoint analysis proposed by Mollinari and Garcia (2019) in a sequence of markers
est_rf_hmm(
input.seq,
input.ph = NULL,
thres = 0.5,
twopt = NULL,
verbose = FALSE,
tol = 1e-04,
est.given.0.rf = FALSE,
reestimate.single.ph.configuration = TRUE,
high.prec = TRUE
)
## S3 method for class 'mappoly.map'
print(x, detailed = FALSE, ...)
## S3 method for class 'mappoly.map'
plot(
x,
left.lim = 0,
right.lim = Inf,
phase = TRUE,
mrk.names = FALSE,
cex = 1,
config = "best",
P = "Parent 1",
Q = "Parent 2",
xlim = NULL,
...
)
input.seq |
an object of class |
input.ph |
an object of class |
thres |
LOD Score threshold used to determine if the linkage phases compared via two-point analysis should be considered. Smaller values will result in smaller number of linkage phase configurations to be evaluated by the multipoint algorithm. |
twopt |
an object of class |
verbose |
if |
tol |
the desired accuracy (default = 1e-04) |
est.given.0.rf |
logical. If TRUE returns a map forcing all recombination fractions equals to 0 (1e-5, for internal use only. Default = FALSE) |
reestimate.single.ph.configuration |
logical. If |
high.prec |
logical. If |
x |
an object of the class |
detailed |
logical. if TRUE, prints the linkage phase configuration and the marker position for all maps. If FALSE (default), prints a map summary |
... |
currently ignored |
left.lim |
the left limit of the plot (in cM, default = 0). |
right.lim |
the right limit of the plot (in cM, default = Inf, i.e., will print the entire map) |
phase |
logical. If |
mrk.names |
if TRUE, marker names are displayed (default = FALSE) |
cex |
The magnification to be used for marker names |
config |
should be |
P |
a string containing the name of parent P |
Q |
a string containing the name of parent Q |
xlim |
range of the x-axis. If |
This function first enumerates a set of linkage phase configurations
based on two-point recombination fraction information using a threshold
provided by the user (argument thresh
). After that, for each
configuration, it reconstructs the genetic map using the
HMM approach described in Mollinari and Garcia (2019). As result, it returns
the multipoint likelihood for each configuration in form of LOD Score comparing
each configuration to the most likely one. It is recommended to use a small number
of markers (e.g. 50 markers for hexaploids) since the possible linkage
phase combinations bounded only by the two-point information can be huge.
Also, it can be quite sensible to small changes in 'thresh'
.
For a large number of markers, please see est_rf_hmm_sequential
.
A list of class mappoly.map
with two elements:
i) info: a list containing information about the map, regardless of the linkage phase configuration:
ploidy |
the ploidy level |
n.mrk |
number of markers |
seq.num |
a vector containing the (ordered) indices of markers in the map, according to the input file |
mrk.names |
the names of markers in the map |
seq.dose.p1 |
a vector containing the dosage in parent 1 for all markers in the map |
seq.dose.p2 |
a vector containing the dosage in parent 2 for all markers in the map |
chrom |
a vector indicating the sequence (usually chromosome) each marker belongs
as informed in the input file. If not available,
|
genome.pos |
physical position (usually in megabase) of the markers into the sequence |
seq.ref |
reference base used for each marker (i.e. A, T, C, G). If not available,
|
seq.alt |
alternative base used for each marker (i.e. A, T, C, G). If not available,
|
chisq.pval |
a vector containing p-values of the chi-squared test of Mendelian segregation for all markers in the map |
data.name |
name of the dataset of class |
ph.thres |
the LOD threshold used to define the linkage phase configurations to test |
ii) a list of maps with possible linkage phase configuration. Each map in the list is also a list containing
seq.num |
a vector containing the (ordered) indices of markers in the map, according to the input file |
seq.rf |
a vector of size ( |
seq.ph |
linkage phase configuration for all markers in both parents |
loglike |
the hmm-based multipoint likelihood |
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_. https://doi.org/10.1534/g3.119.400378
mrk.subset <- make_seq_mappoly(hexafake, 1:10)
red.mrk <- elim_redundant(mrk.subset)
unique.mrks <- make_seq_mappoly(red.mrk)
subset.pairs <- est_pairwise_rf(input.seq = unique.mrks,
ncpus = 1,
verbose = TRUE)
## Estimating subset map with a low tolerance for the E.M. procedure
## for CRAN testing purposes
subset.map <- est_rf_hmm(input.seq = unique.mrks,
thres = 2,
twopt = subset.pairs,
verbose = TRUE,
tol = 0.1,
est.given.0.rf = FALSE)
subset.map
## linkage phase configuration with highest likelihood
plot(subset.map, mrk.names = TRUE, config = "best")
## the second one
plot(subset.map, mrk.names = TRUE, config = 2)
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