create_phased_maplist: Create a phased homologue map list using the original dosages
In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

create_phased_maplist is a function for creating a phased maplist, using integrated map positions and original marker dosages.

create_phased_maplist(maplist, dosage_matrix.conv, dosage_matrix.orig = NULL,
  remove_markers = NULL, N_linkages = 2, lower_bound = 0.05, ploidy = 4,
  ploidy2 = NULL, marker_assignment.1, marker_assignment.2,
  original_coding = FALSE, log = NULL, verbose = TRUE)

`maplist`	A list of maps. In the first column marker names and in the second their position.
`dosage_matrix.conv`	Matrix of martker dosage scores with markers in rows and individuals in columns. Note that dosages must be in converted form, i.e. after having run the `convert_marker_dosages` function. Errors may result otherwise.
`dosage_matrix.orig`	Optional, by default `NULL`.The unconverted dosages (i.e. raw dosage data before using the `convert_marker_dosages` function). Required if `original_coding` is `TRUE`.
`remove_markers`	Optional vector of marker names to remove from the maps. Default is `NULL`.
`N_linkages`	Number of significant linkages (as defined in `homologue_lg_assignment`) required for high-confidence linkage group assignment.
`lower_bound`	Numeric. Lower bound for the rate at which homologue linkages (fraction of total for that marker) are recognised.
`ploidy`	Integer. Ploidy of the organism.
`ploidy2`	Optional integer, by default `NULL`. Ploidy of parent 2, if different from parent 1.
`marker_assignment.1`	A marker assignment matrix for parent 1 with markernames as rownames and at least containing the column `"Assigned_LG"`.
`marker_assignment.2`	A marker assignment matrix for parent 2 with markernames as rownames and at least containing the column `"Assigned_LG"`.
`original_coding`	Logical. Should the phased map use the unconverted dosage coding or not?
`log`	Character string specifying the log filename to which standard output should be written. If `NULL` log is send to stdout.
`verbose`	Logical, by default `TRUE`. Should unphased markers be recorded?

data("integrated.maplist", "ALL_dosages", "marker_assignments_P1","marker_assignments_P2")
create_phased_maplist(integrated.maplist,
                     dosage_matrix.conv = ALL_dosages,
                     marker_assignment.1=marker_assignments_P1,
                     marker_assignment.2=marker_assignments_P2)