make_one_map: Consolidate and prepare map data for synteny block detection

In ksamuk/syntR: Detection of synteny blocks via comparison of genetics maps

Description

Consolidate and prepare map data for synteny block detection

Usage

make_one_map(map, space_size = 20, map1_chr_order = NULL,
  map2_chr_order = NULL, map1_max_chr_lengths = NULL,
  map2_max_chr_lengths = NULL, flip_chrs = NULL)

Arguments

map	data frame, contains marker order and chromosome assignments for markers in both maps
space_size	numeric, the amount of space to pad markers between linkage groups
map1_chr_order	numeric, optional: the numeric order in which to display markers in map1
map2_chr_order	numeric, optional: the numeric order in which to display markers in map2
map1_max_chr_lengths	numeric, optional: values of the total lengths of each linkage group in map1. useful when markers do not span known extent of linkage groups.
map2_max_chr_lengths	numeric, optional: values of the total lengths of each linkage group in map2. useful when markers do not span known extent of linkage groups.
flip_chrs	logical, optional: a vector of TRUE/FALSE indicating which linkage groups should be flipped (for display purposes only)

Value

a 'map list': a list of length 5 containing consolidated/flipped/reordered markers for both maps

ksamuk/syntR documentation built on Feb. 11, 2021, 4:46 a.m.