clusterOrderCross: Group markers into blocks and arrange those blocks

In mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description

Group markers into blocks and arrange those blocks

Usage

clusterOrderCross(
  mpcrossLG,
  cool = 0.5,
  tmin = 0.1,
  nReps = 1,
  maxMove = 0,
  effortMultiplier = 1,
  randomStart = TRUE,
  nGroups
)

Arguments

mpcrossLG	An object of class mpcrossLG, containing genetic data and linkage groups.
cool	Rate of cooling
tmin	Minimum temperature
nReps	Number of independent replications of the simulated annealing algorithm
maxMove	Maximum number of positions by which to shift a single marker, as part of the simulated annealing. A value of zero indicates no limit.
effortMultiplier	Multiplier for the amount of computational effort
randomStart	If TRUE, start from the current ordering
nGroups	The number of groups to form using hierarchical clustering

Details

In some cases the number of markers is too large to reorder all markers on a chromosome. However, the problem becomes more tractable if the markers are already in a roughly correct ordering to start with. This function is intended to generate that roughly accurate ordering, and then subsequenty local reordering using orderCross can be applied to generate a final marker ordering.

The rough ordering is generated by forming some number of groups of markers, using hierarchical clustering. A consensus disimilarity between every group of markers is formed, and this is used to order the groups. That is, we decide whether the markers will be ordered as group 1, group 2, group 3, etc, or group 2, group 1, group 3, etc. The ordering of the markers within each group is unchanged.

Value

An object of class mpcrossLG, identical to the input except with the markers rearranged.

mpMap2 documentation built on Sept. 13, 2020, 5:17 p.m.