infoGeneticMap: Info about a given genetic map

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Info about a given genetic map

Description

Returns some information on a given genetic map, notably the relations between linkage groups and chromosomes. Beforehand, the genetic map can be filtered.

Usage

infoGeneticMap(
  genmap,
  min.mrks.per.lg = 0,
  min.mrks.per.chr.in.lg = 0,
  chrs.todrop = NULL,
  verbose = 1
)

Arguments

genmap	data frame with at least three columns named "linkage.group", "locus" and "chr", and one row per locus
min.mrks.per.lg	to filter the genetic map, any linkage group with strictly less than this threshold will be discarded
min.mrks.per.chr.in.lg	to filter the genetic map, for linkage groups with markers belonging to several chromosomes, any marker belonging to chromosomes with stricly less than this threshold will be discarded
chrs.todrop	optional vector of chromosome names to drop from the analysis
verbose	verbosity level (0/1/2)

Value

list with several summaries, as well as a clean version of the genetic map with one linkage group per chromosome (among the most represented)

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.