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

create_phased_maplist

R Documentation

Create a phased homologue map list using the original dosages

Description

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

Usage

create_phased_maplist(
  input_type = "discrete",
  maplist,
  dosage_matrix.conv,
  dosage_matrix.orig = NULL,
  probgeno_df,
  chk,
  remove_markers = NULL,
  original_coding = FALSE,
  N_linkages = 2,
  lower_bound = 0.05,
  ploidy,
  ploidy2 = NULL,
  marker_assignment.1,
  marker_assignment.2,
  parent1 = "P1",
  parent2 = "P2",
  marker_conversion_info = NULL,
  log = NULL,
  verbose = TRUE
)

Arguments

`input_type`	Can be either one of 'discrete' or 'probabilistic'. For the former (default), at least `dosage_matrix.conv` must be supplied, while for the latter `chk` must be supplied.
`maplist`	A list of maps. In the first column marker names and in the second their position.
`dosage_matrix.conv`	Matrix of marker 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`.
`probgeno_df`	Probabilistic genotypes, for description see e.g. `gp_overview`. Required if probabilistic genotypes are used.
`chk`	Output list as returned by function `checkF1`. Required if probabilistic genotypes are used.
`remove_markers`	Optional vector of marker names to remove from the maps. Default is `NULL`.
`original_coding`	Logical. Should the phased map use the original marker coding or not? By default `FALSE`.
`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"`.
`parent1`	character vector with names of the samples of parent 1
`parent2`	character vector with names of the samples of parent 2
`marker_conversion_info`	One of the list elements generated by the function `convert_marker_dosages`. Required if `original_coding` is `TRUE`.
`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 details of the phasing process be given?

Examples

## Not run: 
data("integrated.maplist", "screened_data3", "marker_assignments_P1","marker_assignments_P2")
create_phased_maplist(maplist = integrated.maplist,
                     dosage_matrix.conv = screened_data3,
                     marker_assignment.1=marker_assignments_P1,
                     marker_assignment.2=marker_assignments_P2,
                     ploidy = 4)
## End(Not run)

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.