try_seq_by_seq: Run try_seq considering previous sequence
In onemap: Construction of Genetic Maps in Experimental Crosses

try_seq_by_seq

R Documentation

Run try_seq considering previous sequence

Description

It uses try_seq function repeatedly trying to positioned each marker in a vector of markers into a already ordered sequence. Each marker in the vector "markers" is kept in the sequence if the difference of LOD and total group size of the models with and without the marker are below the thresholds "lod.thr" and "cM.thr".

Usage

try_seq_by_seq(sequence, markers, cM.thr = 10, lod.thr = -10, verbose = TRUE)

Arguments

`sequence`	object of class sequence with ordered markers
`markers`	vector of integers defining the marker numbers to be inserted in the `sequence`
`cM.thr`	number defining the threshold for total map size increase when inserting a single marker
`lod.thr`	the difference of LODs between model before and after inserting the marker need to have value higher than the value defined in this argument
`verbose`	A logical, if TRUE it output progress status information.

Value

An object of class sequence, which is a list containing the following components:

`seq.num`	a `vector` containing the (ordered) indices of markers in the sequence, according to the input file.
`seq.phases`	a `vector` with the linkage phases between markers in the sequence, in corresponding positions. `-1` means that there are no defined linkage phases.
`seq.rf`	a `vector` with the recombination frequencies between markers in the sequence. `-1` means that there are no estimated recombination frequencies.
`seq.like`	log-likelihood of the corresponding linkage map.
`data.name`	name of the object of class `onemap` with the raw data.
`twopt`	name of the object of class `rf_2pts` with the 2-point analyses.