filter_2pts_gaps function

Filter markers based on 2pts distance

filter_2pts_gaps(input.seq, max.gap = 10)

Arguments

• input.seq: object of class sequence with ordered markers
• max.gap: maximum gap measured in kosambi centimorgans allowed between adjacent markers. Markers that presents the defined distance between both adjacent neighbors will be removed.

Returns

New sequence 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: object of class onemap with the raw data. - twopt: object of class rf_2pts with the 2-point analyses.

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu