consensus_LG_assignment: Consensus LG assignment

In polymapR: Linkage Analysis in Outcrossing Polyploids

Consensus LG assignment

Description

Assign markers to an LG based on consensus between two parents.

Usage

consensus_LG_assignment(
  P1_assigned,
  P2_assigned,
  LG_number,
  ploidy,
  consensus_file = NULL,
  log = NULL
)

Arguments

P1_assigned	A marker assignment file of the first parent. Should contain the number of linkages per LG per marker.
P2_assigned	A marker assignment file of the second parent. Should be the same markertype as first parent and contain the number of linkages per LG per marker.
LG_number	Number of linkage groups (chromosomes).
ploidy	Ploidy level of plant species.
consensus_file	Filename of consensus output. No output is written if NULL.
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

Returns a list containing the following components:

P1_assigned	A (modified) marker assignment matrix of the first parent.
P2_assigned	A (modified) marker assignment matrix of the second parent.

Examples

data("P1_SxS_Assigned", "P2_SxS_Assigned_2")
SxS_Assigned_list <- consensus_LG_assignment(P1_SxS_Assigned,P2_SxS_Assigned_2,5,4)

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