count_recombinations: Predict recombination breakpoints using IBD probabilities
In polyqtlR: QTL Analysis in Autopolyploid Bi-Parental F1 Populations

Description Usage Arguments Value Examples

The function count_recombinations returns a list of all predicted recombination breakpoints. The output can be passed using the argument recombination_data to the function visualiseHaplo, where the predicted breakpoints overlay the haplotypes. Alternatively, a genome-wide visualisation of the recombination landscape both per linkage group and per individual can be generated using the function plotRecLS, which can be useful in identifying problematic areas of the linkage maps, or problematic individuals in the population. Currently, recombination break-points are only estimated from bivalents in meiosis; any offspring resulting from a predicted multivalent is excluded from the analysis and will be returned with a NA value.

1	count_recombinations(IBD_list, plausible_pairing_prob = 0.4)

IBD_list

List of IBD_probabilities as estimated using one of the various methods available (e.g. estimate_IBD).

plausible_pairing_prob

The minimum probability of a pairing configuration needed to analyse an individual's IBD data. The default setting of 0.4 is rather low - but accommodates scenarios where e.g. two competing plausible pairing scenarios are possible. In such situations, both pairing configurations (also termed "valencies") would be expected to have a probability close to 0.5. Both are then considered, and the output contains the probability of both situations. These can then be used to generate a probabilistic recombination landscape. If a more definite set of predictions is required, simply increase plausible_pairing_prob to eliminate such uncertainty. These individuals will then be returned with a NA value.

A nested list corresponding to each linkage group. Within each LG, a list with 3 items is returned, specifying the plausible_pairing_prob, the map and the predicted recombinations in each individual in the mapping population. Per individual, all valencies with a probability greater than plausible_pairing_prob are returned, specifying both the Valent_probability and the best estimate of the cM position of the recombination_breakpoints involving pairs of homologues A, B, C etc. (in the order parent 1, parent 2). If no recombinations are predicted, a NA value is given instead.