Description Usage Arguments Value Examples
View source: R/exported_functions.R
cluster_SN_markers
clusters simplex nulliplex at different LOD scores.
1 2 3 4 | cluster_SN_markers(linkage_df, LOD_sequence = 7, independence_LOD = FALSE,
LG_number = 5, ploidy = 4, parentname = "", plot_network = F,
min_clust_size = 1, plot_clust_size = TRUE, max_vertex_size = 5,
min_vertex_size = 2, phase_considered = "All", log = NULL)
|
linkage_df |
A linkage data.frame as output of |
LOD_sequence |
A numeric vector. Specifying a sequence of LOD thresholds at which clustering is performed. |
independence_LOD |
Logical. Should the LOD of independence be used for clustering? (by default, |
LG_number |
Expected number of chromosomes (linkage groups) |
ploidy |
Ploidy level of the plant species |
parentname |
Name of parent |
plot_network |
Logical. Should a network be plotted. Recommended FALSE with large number of marker combinations. |
min_clust_size |
Integer. The minimum cluster size to be plotted. This does not delete clusters. All clusters are returned. |
plot_clust_size |
Logical. Should exact cluster size be plotted as vertex labels? |
max_vertex_size |
Integer. The maximum vertex size. Only used if |
min_vertex_size |
Integer. The minimum vertex size. Only used if |
phase_considered |
Character string. By default all phases are used, but "coupling" or "repulsion" are also allowed. |
log |
Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout (console). |
A list with cluster data.frames.
1 2 | data("SN_SN_P1")
cluster_list<-cluster_SN_markers(SN_SN_P1, LOD_sequence=c(4:10), parentname="P1")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.