phase_SN_diploid: Phase 1.0 markers at the diploid level

In polymapR: Linkage Analysis in Outcrossing Polyploids

Phase 1.0 markers at the diploid level

Description

phase_SN_diploid phases simplex x nulliplex markers for a diploid parent.

Usage

phase_SN_diploid(
  linkage_df,
  cluster_list,
  LOD_chm = 3.5,
  LG_number,
  independence_LOD = FALSE,
  log = NULL
)

Arguments

linkage_df	A linkage data.frame as output of linkage calculating linkage between 1.0 markers.
cluster_list	A list of cluster_stacks, the output of cluster_SN_markers.
LOD_chm	Integer. The LOD threshold specifying at which LOD score the markers divide into chromosomal groups
LG_number	Expected number of chromosomes (linkage groups)
independence_LOD	Logical. Should the LOD of independence be used for clustering? (by default, FALSE.)
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout (console).

Value

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

Examples

data("SN_SN_P2_triploid","P2_homologues_triploid")
cluster_list2<-phase_SN_diploid(SN_SN_P2_triploid,P2_homologues_triploid,LOD_chm=5,LG_number = 3)

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