View source: R/polyqtlR_functions.R

count_recombinations | R Documentation |

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.

```
count_recombinations(IBD_list, plausible_pairing_prob = 0.3)
```

`IBD_list` |
List of IBD_probabilities as estimated using one of the various methods available (e.g. |

`plausible_pairing_prob` |
The minimum probability of a pairing configuration needed to analyse an individual's IBD data.
The default setting of 0.3 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. In some cases,
it may not be possible to discern the pairing in one of the parents due to a lack of recombination (ie. full parental haplotypes were transmitted). In such cases,
having a lower threshold here will allow more offspring to be analysed without affecting the quality of the predictions. If a more definite
set of predictions is required, simply increase |

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.

```
data("IBD_4x")
recom.ls <- count_recombinations(IBD_4x)
```

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