assign_linkage_group {polymapR}

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)