cluster_SN_markers {polymapR}

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 = FALSE,
  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 parent for which clustering is to be performed

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 returned. By default, a minimum cluster size of 1 is used, meaning all markers are returned. Setting this to a higher number can be useful for cleaning out mini-clusters that don't show strong linkage to the rest of the marker set.

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)