try_seq_by_seq function

Run try_seq considering previous sequence

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".

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.

Returns

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.