assign_linkage_group: Assign non-SN markers to a linkage group and homologue(s).

In polymapR: Linkage Analysis in Outcrossing Polyploids

Assign non-SN markers to a linkage group and homologue(s).

Description

assign_linkage_group quantifies per marker number of linkages to a linkage group and evaluates to which linkage group (and homologue(s)) the marker belongs.

Usage

assign_linkage_group(
  linkage_df,
  LG_hom_stack,
  SN_colname = "marker_a",
  unassigned_marker_name = "marker_b",
  phase_considered = "coupling",
  LG_number,
  LOD_threshold = 3,
  ploidy,
  assign_homologue = T,
  log = NULL
)

Arguments

linkage_df	A linkage data.frame as output of linkage.
LG_hom_stack	A data.frame with markernames ("SxN_Marker"), linkage group ("LG") and homologue ("homologue")
SN_colname	The name of the column in linkage_df harbouring the 1.0 markers
unassigned_marker_name	The name of the column in linkage_df harbouring the marker that are to be assigned.
phase_considered	The phase that is used to assign the markers (deprecated)
LG_number	The number of chromosomes (linkage groups) in the species.
LOD_threshold	The LOD score at which a linkage to a linkage group is significant.
ploidy	The ploidy of the plant species.
assign_homologue	Logical. Should markers be assigned to homologues? If FALSE markers will be assigned to all homologues
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

Output is a data.frame with at least the following columns:

Assigned_LG	The assigned linkage group
Assigned_hom1	The homologue with most linkages

The columns LG1 - LGn and Hom1 - Homn give the number of hits per marker for that linkage group/homologue. Assigned_hom2 .. gives the nth homologue with most linkages.

Examples

data("SN_DN_P1", "LGHomDf_P1_1")
assigned_df<-assign_linkage_group(linkage_df = SN_DN_P1,
                     LG_hom_stack = LGHomDf_P1_1,
                     LG_number = 5, ploidy = 4)

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