R: Create a sequence of markers

make_seq_mappoly

R Documentation

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 class 'mappoly.sequence'
print(x, ...)

## S3 method for class 'mappoly.sequence'
plot(x, ...)

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

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

Author(s)

Marcelo Mollinari, mmollin@ncsu.edu, with modifications by Gabriel Gesteira, gdesiqu@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_. \Sexpr[results=rd,stage=build]{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)