Description Usage Arguments Value Examples
This function splits markers into linkage groups (LG), which ideally represent chromosomes. The split is based on hierarchical clustering with a single linkage distance.
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rf |
Matrix of pairwise recombination frequencies. |
height |
Threshold value for grouping the markers. |
nchr |
Expected number of chromosomes. |
method |
Default is "single", which is used for the hierarchical clustering. |
filter |
Logical, if the result should be filtered or not. Default is FALSE. Creates zeros for the markers below the threshold. |
thresh |
Threshold for filtering. Default is 0.05, i.e. linkage groups with less than 5% of markers, are filtered out. |
rm.dup |
Logical, if the duplicated markers should be filtered out. TRUE is highly recommended because the markers have no added value for the linkage map. |
Vector of cluster relationship. Same length and order as the matrix of recombination frequencies.
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