estMrkOrderGenDistsWithCarthagene: Estimate marker order and genetic distances with CarthaGene

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

Estimate marker order and genetic distances with CarthaGene

Description

Estimates marker order and genetic distances for a given linkage group with CarthaGene (commands "buildfw", "flips", polish" and "squeeze").

Usage

estMrkOrderGenDistsWithCarthagene(
  cg,
  linkgroups,
  lg.id,
  keep.thresh = 3,
  add.thresh = 3,
  init.order = NULL,
  postprocessing = 1,
  flips.size = 4,
  flips.lod.thresh = 3,
  flips.iter = 1,
  squeeze.thresh = 20,
  mrk2phy = NULL,
  verbose = 1
)

Arguments

cg	list returned by openCarthagene
linkgroups	data frame returned by defLinkgroupsWithCarthagene, towhich a column of logicals named "todrop" may have been added, indicating which marker(s) to drop via "mrkdel" before executing "buildfw"
lg.id	identifier of the linkage group of interest
keep.thresh	the minimum difference in log-likelihood between the best insertion point and the second best insertion point required for the map to be considered in the future
add.thresh	the minimum difference in log-likelihood between the best insertion point and the second best insertion point required for a locus to be insertable; this threshold is also used to filter out the differences in log-likelihood reported by the post-processing option (only differences lower than the threshold will be reported)
init.order	if not NULL, vector containing at least three marker identifiers in a given order to start from
postprocessing	if 0, only framework mapping is performed; if 1, post-processing is also applied (see "add.thresh"); if 2, post-processing is applied only to markers in "mrk.list"
flips.size	size of the sliding window for the "flips" command (cannot exceed 9)
flips.lod.thresh	maximum difference of log-likelihood with the best map so that "flips" reports the permutation
flips.iter	if 1, "flips" will be iterated as long as a new, improved map has been found; specify O, otherwise
squeeze.thresh	distance threshold in cMorgan (Haldane distance) for genetics data or cRay for Radiation Hybrids data used by "squeeze" to expunge non-reliable locus from the map
mrk2phy	named vector which names are the locus and values are the physical distances on the chromosome corresponding to the linkage group of interest
verbose	verbosity level (0/1)

Value

data frame returned by parseCgMaprintd containing the best map for the given linkage group according to CarthaGene, and possibly a column "physical.distance"

Author(s)

Timothee Flutre

See Also

openCarthagene, runCarthagene, defLinkgroupsWithCarthagene, parseCgMaprintd, closeCarthagene

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