mappoly (version 0.4.1)

make_seq_mappoly: Create a Sequence of Markers

Description

Constructs a sequence of markers based on an object belonging to various specified classes. This function is versatile, supporting multiple input types and configurations for generating marker sequences.

Usage

make_seq_mappoly(
  input.obj,
  arg = NULL,
  data.name = NULL,
  info.parent = c("all", "p1", "p2"),
  genomic.info = NULL
)
# S3 method for mappoly.sequence
print(x, ...)
# S3 method for mappoly.sequence
plot(x, ...)

Value

Returns an object of class `mappoly.sequence`, comprising:

"seq.num"

Ordered vector of marker indices according to the input.

"seq.phases"

List of linkage phases between markers; -1 for undefined phases.

"seq.rf"

Vector of recombination frequencies; -1 for not estimated frequencies.

"loglike"

Log-likelihood of the linkage map.

"data.name"

Name of the `mappoly.data` object with raw data.

"twopt"

Name of the `mappoly.twopt` object with 2-point analyses; -1 if not computed.

Arguments

input.obj

An object belonging to one of the specified classes: mappoly.data, mappoly.map, mappoly.sequence, mappoly.group, mappoly.unique.seq, mappoly.pcmap, mappoly.pcmap3d, mappoly.geno.ord, or mappoly.edit.order.

arg

Specifies the markers to include in the sequence, accepting several formats: a string 'all' for all markers; a string or vector of strings 'seqx' where x is the sequence number (0 for unassigned markers); a vector of integers indicating specific markers; or a vector of integers representing linkage group numbers if input.obj is of class mappoly.group. For certain classes (mappoly.pcmap, mappoly.pcmap3d, mappoly.unique.seq, or mappoly.geno.ord), arg can be NULL.

data.name

Name of the mappoly.data class object.

info.parent

Selection criteria based on parental information: 'all' for all dosage combinations, 'P1' for markers informative in parent 1, or 'P2' for markers informative in parent 2. Default is 'all'.

genomic.info

Optional and applicable only to mappoly.group objects. Specifies the use of genomic information in sequence creation. With NULL (default), all markers defined by the grouping function are included. Numeric values indicate the use of specific sequences from genomic information, aiming to match the maximum number of markers with the group. Supports single values or vectors for multiple sequence consideration.

x

An object of 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)