bridgeHomologues {polymapR}

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 bridging-type marker (e.g. 2.0) 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 links between a bridge marker and a cluster for that bridge to be considered. In the case of a 2x0 marker for example, this argument means that the 2x0 marker must have at least min_links linkages of at least a LOD of LOD_threshold with markers from each of the clusters involved, to be considered a single bridging link. Make this number higher if there are a lot of spurious links.

min_bridges

The minimum number of bridge markers needed to assign two homologues together as coming from the same chromosomal linkage group. See argument min_links for further details.

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")