polymapR (version 1.1.5)

create_phased_maplist: 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 (named 'marker_conversion_info') generated by the function convert_marker_dosages when the argument marker_conversion_info was set to TRUE (not the default, so a user will typically have to re-run this step first). 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

if (FALSE) {
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)}