bridgeHomologues: Use bridge markers to cluster homologues into linkage groups

In polymapR: Linkage Analysis in Outcrossing Polyploids

Use bridge markers to cluster homologues into linkage groups

Description

Clustering at high LOD scores results in marker clusters representing homologues. bridgeHomologues clusters these (pseudo)homologues to linkage groups using linkage information between 1.0 and bridge markers within a parent (e.g. 2.0 for a tetraploid). If parent-specific bridge markers (e.g. 2.0) cannot be used, biparental markers can also be used (e.g. 1.1, 1.2, 2.1, 2.2 and 1.3 markers). The linkage information between 1.0 and biparental markers can be combined.

Usage

bridgeHomologues(
  cluster_stack,
  cluster_stack2 = NULL,
  linkage_df,
  linkage_df2 = NULL,
  LOD_threshold = 5,
  automatic_clustering = TRUE,
  LG_number,
  parentname = "",
  min_links = 1,
  min_bridges = 1,
  only_coupling = FALSE,
  log = NULL
)

Arguments

cluster_stack	A data.frame with a column "marker" specifying markernames, and a column "cluster" specifying marker cluster
cluster_stack2	Optional. A cluster_stack for the other parent. Use this argument if cross-parent markers are used (e.g. when using 1.1 markers).
linkage_df	A linkage data.frame as output of linkage between bridge (e.g. 1.0 and 2.0) markers.
linkage_df2	Optional. A linkage_df specifying linkages between 1.0 and cross-parent markers in the other parent. Use this argument if cross-parent markers are used (e.g. when using 1.1, 2.1, 1.2 and/or 2.2 markers). The use of multiple types of cross-parent markers is allowed.
LOD_threshold	Integer. The LOD threshold specifying at which LOD score a link between 1.0 and bridge (e.g. 2.0) markers is used for clustering homologues.
automatic_clustering	Logical. Should clustering be executed without user input?
LG_number	Integer. Expected number of chromosomes (linkage groups)
parentname	Name of the parent. Used in the main title of the plot.
min_links	The minimum number of cross-parent linkages for a marker to be considered. Make this number higher if there are a lot of spurious links.
min_bridges	The minimum number of linking markers to link two homologues together.
only_coupling	Logical, should only coupling linkages be used in the process? By default FALSE
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

A data.frame with markers classified by homologue and linkage group.

Examples

data("P1_homologues", "P2_homologues", "SN_DN_P1", "SN_SS_P1", "SN_SS_P2")
ChHomDf<-bridgeHomologues(cluster_stack = P1_homologues[["5"]],
                 linkage_df=SN_DN_P1,
                 LOD_threshold=4,
                 automatic_clustering=TRUE,
                 LG_number=5,
                 parentname="P1")

ChHomDf<-bridgeHomologues(cluster_stack = P1_homologues[["5"]],
                           cluster_stack2 = P2_homologues[["5"]],
                 linkage_df=SN_SS_P1,
                 linkage_df2=SN_SS_P2,
                 LOD_threshold=4,
                 automatic_clustering=TRUE,
                 LG_number=5,
                 parentname="P1")

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