mappoly (version 0.3.3)

make_seq_mappoly: Create a sequence of markers

Description

Makes a sequence of markers based on an object of another class.

Usage

make_seq_mappoly(input.obj, arg = NULL, data.name = NULL, genomic.info = NULL)
# S3 method for mappoly.sequence
print(x, ...)
# S3 method for mappoly.sequence
plot(x, ...)

Value

An object of class mappoly.sequence, which is a list containing the following components:

seq.num

a vector containing the (ordered) indices of markers in the sequence, according to the input file

seq.phases

a list with the linkage phases between markers in the sequence, in corresponding positions. -1 means that there are no defined linkage phases

seq.rf

a vector with the recombination frequencies between markers in the sequence. -1 means that there are no estimated recombination frequencies

loglike

log-likelihood of the corresponding linkage map

data.name

name of the object of class mappoly.data with the raw data

twopt

name of the object of class mappoly.twopt with the 2-point analyses. -1 means that the twopt estimates were not computed

Arguments

input.obj

an object of one of the following classes: mappoly.data, mappoly.map, mappoly.group, mappoly.unique.seq, mappoly.pcmap, mappoly.pcmap3d, or mappoly.geno.ord

arg

can be one of the following objects: i) a string 'all', resulting in a sequence with all markers in the raw data; ii) a string or a vector of strings 'seqx', where x is the sequence (x = 0 indicates unassigned markers); iii) a vector of integers specifying which markers comprise the sequence; iv) an integer representing linkage group if input.object has class mappoly.group; or v) NULL if input.object has class mappoly.pcmap, mappoly.pcmap3d, mappoly.unique.seq, or mappoly.geno.ord

data.name

name of the object of class mappoly.data

genomic.info

optional argument applied for mappoly.group objects only. This argument can be NULL, or can hold the numeric combination of sequences from genomic information to be used when making the sequences. When genomic.info = NULL (default), the function returns a sequence containing all markers defined by the grouping function. When genomic.info = 1, the function returns a sequence with markers that matched the intersection between grouping function and genomic information, considering the sequence from genomic information that holds the maximum number of markers matching the group; when genomic.info = c(1,2), the function returns a sequence with markers that matched the intersection between grouping function and genomic information, considering two sequences from genomic information that presented the maximum number of markers matching the group; and so on.

x

an object of the class mappoly.sequence

...

currently ignored

Author

Marcelo Mollinari, , with modifications by Gabriel Gesteira,

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

    all.mrk <- make_seq_mappoly(hexafake, 'all')
    seq1.mrk <- make_seq_mappoly(hexafake, 'seq1')
    plot(seq1.mrk)
    some.mrk.pos <- c(1,4,28,32,45)
    (some.mrk.1 <- make_seq_mappoly(hexafake, some.mrk.pos))
    plot(some.mrk.1)