ls_linkage_phases: List of linkage phases

In mappoly: Genetic Linkage Maps in Autopolyploids

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 class 'two.pts.linkage.phases'
print(x, ...)

## S3 method for class 'two.pts.linkage.phases'
plot(x, ...)

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

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

Author(s)

Marcelo Mollinari, [e-mail]

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_. doi: 10.1534/g3.119.400378

Examples

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)

mappoly documentation built on Jan. 6, 2023, 1:16 a.m.