polymapR (version 1.1.2)

merge_marker_assignments: Merge marker assignments

Description

merge_marker_assignments Merges 1.0 backbone object with marker assignment objects

Usage

merge_marker_assignments(
  dosage_matrix,
  target_parent = "P1",
  other_parent = "P2",
  LG_hom_stack,
  SN_linked_markers,
  ploidy,
  LG_number,
  log = NULL
)

Value

Returns a matrix with marker assignments. Number of linkages of 1.0 markers are artificial.

Arguments

dosage_matrix

An integer matrix with markers in rows and individuals in columns.

target_parent

Character string specifying target parent.

other_parent

Character string specifying other parent.

LG_hom_stack

data.frame specifying 1.0 marker assignments to linkage groups and homologues.

SN_linked_markers

a list of marker assignment objects

ploidy

Ploidy level of plant species.

LG_number

Number of linkage groups (chromosomes).

log

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Examples

data("screened_data3", "LGHomDf_P1_1", "P1_SxS_Assigned", "P1_DxN_Assigned")
merged_assignment<-merge_marker_assignments(screened_data3, target_parent="P1",
                         other_parent="P2",
                         LG_hom_stack=LGHomDf_P1_1,
                         SN_linked_markers=list(P1_SxS_Assigned, P1_DxN_Assigned),
                         ploidy=4,
                         LG_number=5)