defLinkgroupsWithCarthagene: Define linkage groups with CarthaGene

View source: R/CarthaGene.R

defLinkgroupsWithCarthageneR Documentation

Define linkage groups with CarthaGene

Description

Defines linkage groups with CarthaGene ("group" command), so that two markers whose 2-point Haldane distance is below the given distance threshold, and 2-point LOD is above the LOD threshold, will be put in the same linkage group. Choose these thresholds by trial and error until it makes sense given the ploidy of the species of interest.

Usage

defLinkgroupsWithCarthagene(
  file = NULL,
  task.id = NULL,
  cg = NULL,
  dist.thresh = 0.3,
  lod.thresh = 3,
  mrk2chr = NULL,
  close.cg = FALSE,
  verbose = 1
)

Arguments

file

path to the file containing the dataset (used if cg is NULL)

task.id

identifier of the task (used if cg is NULL)

cg

list returned by openCarthagene (used if file and task.id are NULL)

dist.thresh

distance threshold

lod.thresh

LOD threshold

mrk2chr

named vector which values are markers and names are chromosomes

close.cg

if TRUE, the connection to CarthaGene will be closed and the temporary file removed

verbose

verbosity level (0/1)

Value

data frame returned by parseCgGroup, with at least three columns, "linkage.group", "id" and "locus", and another column, "chr", if mrk2chr is provided

Author(s)

Timothee Flutre

See Also

openCarthagene, runCarthagene, parseCgMrkinfo, parseCgGroup, closeCarthagene


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