generate_all_link_phases_elim_equivalent_haplo: Eliminate equivalent linkage phases

In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

Eliminate equivalent linkage phases

Description

Generates all possible linkage phases between two blocks of markers (or a block and a marker), eliminating equivalent configurations, i.e. configurations with the same likelihood and also considering the two-point information (shared alleles)

Usage

generate_all_link_phases_elim_equivalent_haplo(
  block1,
  block2,
  rf.matrix,
  ploidy,
  max.inc = NULL
)

Arguments

block1	submap with markers of the first block
block2	submap with markers of the second block, or just a single marker identified by its name
rf.matrix	matrix obtained with the function rf_list_to_matrix using the parameter shared.alleles = TRUE
ploidy	ploidy level (i.e. 4, 6 and so on)
max.inc	maximum number of allowed inconsistencies (default = NULL: don't check inconsistencies)

Author(s)

Marcelo Mollinari, [e-mail] and Gabriel Gesteira, [e-mail]

mmollina/MAPPoly documentation built on March 8, 2024, 2:04 a.m.