ls_linkage_phases: List of linkage phases

Description

Returns a list of possible linkage phase configurations using the two-point information contained in the object mappoly.twopt as elimination criteria

Usage

ls_linkage_phases(input.seq, thres, twopt, mrk.to.add = NULL, prev.info = NULL)
# S3 method for two.pts.linkage.phases
print(x, ...)
# S3 method for two.pts.linkage.phases
plot(x, ...)

Value

An object of class two.pts.linkage.phases which contains the following structure:

config.to.test: a matrix with all possible linkage phase configurations for both parents, P and Q
rec.frac: a matrix with all recombination fractions
ploidy: the ploidy level
seq.num: the sequence of markers
thres: the LOD threshold
data.name: the dataset name

Arguments

input.seq: an object of class mappoly.sequence
thres: the LOD threshold used to determine whether linkage phases compared via two-point analysis should be considered
twopt: an object of class mappoly.twopt containing the two-point information
mrk.to.add: marker to be added to the end of the linkage group. If NULL (default) adds all markers contained in input.seq. Mostly for internal usage
prev.info: (optional) an object of class two.pts.linkage.phases containing the previous info about linkage phase configuration. Mostly for internal usage
x: an object of the class two.pts.linkage.phases
...: currently ignored

Author

Marcelo Mollinari, mmollin@ncsu.edu

References

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_. tools:::Rd_expr_doi("10.1534/g3.119.400378")

Examples

Run this code

seq.all.mrk <- make_seq_mappoly(hexafake, 'all')
id <- get_genomic_order(seq.all.mrk)
s <- make_seq_mappoly(id)
seq10 <- make_seq_mappoly(hexafake, s$seq.mrk.names[1:10])
twopt <- est_pairwise_rf(seq10)

## Using the first 10 markers 
l10.seq.3.0 <- ls_linkage_phases(input.seq = seq10, thres = 3, twopt = twopt)
l10.seq.3.0
plot(l10.seq.3.0)
l10.seq.2.0 <- ls_linkage_phases(input.seq = seq10, thres = 2.0, twopt = twopt)
l10.seq.2.0
plot(l10.seq.2.0)
l10.seq.1.0 <- ls_linkage_phases(input.seq = seq10, thres = 1.0, twopt = twopt)
l10.seq.1.0
plot(l10.seq.1.0)

## Using the first 5 markers 
seq5 <- make_seq_mappoly(hexafake, s$seq.mrk.names[1:5])
l5.seq.5.0 <- ls_linkage_phases(input.seq = seq5, thres = 5, twopt = twopt)
l5.seq.5.0
plot(l5.seq.5.0)
l5.seq.3.0 <- ls_linkage_phases(input.seq = seq5, thres = 3, twopt = twopt)
l5.seq.3.0
plot(l5.seq.3.0)
l5.seq.1.0 <- ls_linkage_phases(input.seq = seq5, thres = 1, twopt = twopt)
l5.seq.1.0
plot(l5.seq.1.0)

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