check_marker_assignment: Check for consistent marker assignment between both parents

In polymapR: Linkage Analysis in Outcrossing Polyploids

Check for consistent marker assignment between both parents

Description

Function to ensure there is consistent marker assignment to chromosomal linkage groups for biparental markers

Usage

check_marker_assignment(
  marker_assignment.P1,
  marker_assignment.P2,
  log = NULL,
  verbose = TRUE
)

Arguments

marker_assignment.P1	A marker assignment matrix for parent 1 with markernames as rownames and at least containing the column "Assigned_LG"; the output of homologue_lg_assignment.
marker_assignment.P2	A marker assignment matrix for parent 2 with markernames as rownames and at least containing the column "Assigned_LG"; the output of homologue_lg_assignment.
log	Character string specifying the log filename to which standard output should be written. If NULL (by default) log is send to stdout.
verbose	Should messages be sent to stdout or log?

Value

Returns a list of matrices with corrected marker assignments.

Examples

data("marker_assignments_P1"); data("marker_assignments_P2")
check_marker_assignment(marker_assignments_P1,marker_assignments_P2)

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