Description Usage Arguments Value Examples
View source: R/exported_functions.R
phase_SN_diploid
phases simplex x nulliplex markers for a diploid parent.
1 2 | phase_SN_diploid(linkage_df, cluster_list, LOD_chm = 3.5, LG_number = 3,
independence_LOD = FALSE, log = NULL)
|
linkage_df |
A linkage data.frame as output of |
cluster_list |
A list of cluster_stacks, the output of |
LOD_chm |
Integer. The LOD threshold specifying at which LOD score the markers divide into chromosomal groups |
LG_number |
Expected number of chromosomes (linkage groups) |
independence_LOD |
Logical. Should the LOD of independence be used for clustering? (by default, |
log |
Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout (console). |
A data.frame with markers classified by homologue and linkage group.
1 2 | data("SN_SN_P2_triploid","P2_homologues_triploid")
cluster_list2<-phase_SN_diploid(SN_SN_P2_triploid,P2_homologues_triploid,LOD_chm=5)
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