cluster_SN_markers: Cluster 1.0 markers

In polymapR: Linkage Analysis in Outcrossing Polyploids

Cluster 1.0 markers

Description

cluster_SN_markers clusters simplex nulliplex at different LOD scores.

Usage

cluster_SN_markers(
  linkage_df,
  LOD_sequence = 7,
  independence_LOD = FALSE,
  LG_number,
  ploidy,
  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
)

Arguments

linkage_df	A linkage data.frame as output of linkage calculating linkage between 1.0 markers.
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, FALSE.)
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 plot_clust_size=FALSE.
min_vertex_size	Integer. The minimum vertex size. Only used if plot_clust_size=FALSE.
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).

Value

A (named) list of cluster stacks, each of which is a data.frame with columns "marker" and "cluster"

Examples

data("SN_SN_P1")
cluster_list<-cluster_SN_markers(SN_SN_P1,LOD_sequence=c(4:10),parentname="P1",ploidy=4,LG_number=5)

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.