merge_marker_assignments: Merge marker assignments

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

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 = 5, log = NULL)

Arguments

dosage_matrix	A dosage matrix.
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.

Value

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

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)

mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.