formGroups: Form linkage groups
In rohan-shah/mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description Usage Arguments Details Value

Group markers into linkage groups using hierarchical clustering.

formGroups(
  mpcrossRF,
  groups,
  clusterBy = "theta",
  method = "average",
  preCluster = FALSE
)

`mpcrossRF`	An object of class `mpcrossRF`.
`groups`	The number of groups to form
`clusterBy`	The matrix to use for clustering. The three choices are theta (recombination fractions), lod (log-odds ratio) or combined (a combination of both).
`method`	The method to use for hierarchical cluster. Choices are average, complete and single.
`preCluster`	Before clustering is performed, should we form groups of markers which are completely linked?

This function groups markers into the specified number of linkage groups, using hierarchical clustering. This can be done using three different dissimilarity matrices, specified by the clusterBy argument. If "theta" is specified, then the matrix of recombination fractions is used. If "lod" is specified, then a matrix of likelihood ratio test statistics is used. The hypothesis being tested is whether the recombination fraction is 0.5 (no linkage). If "combined" is specified, then a combination of both previous approaches is used. We recommend the default value of "theta".

The linkage method for hierachical clustering is specified by the method argument; acceptable values are "average", "complete" and "single".

Argument preCluster determines whether the code combines markers that are completely linked, before performing hierarchical clustering. This can lead to speed-ups in clustering truly huge datasets.

An object of class mpcrossLG, containing all the information in the input object and also information about linkage groups.

rohan-shah/mpMap2 documentation built on July 21, 2020, 8:58 p.m.