Description Usage Arguments Details Value See Also Examples

View source: R/TargetingModels.R

`calcTargetingDistance`

converts either the targeting rates in a `TargetingModel`

model to a matrix of 5-mer to single-nucleotide mutation distances, or the substitution
rates in a 1-mer substitution model to a symmetric distance matrix.

1 | ```
calcTargetingDistance(model, places = 2)
``` |

`model` |
TargetingModel object with mutation likelihood information, or a 4x4 1-mer substitution matrix normalized by row with rownames and colnames consisting of "A", "T", "G", and "C". |

`places` |
decimal places to round distances to. |

The targeting model is transformed into a distance matrix by:

Converting the likelihood of being mutated

*p=mutability*substitution*to distance*d=-log10(p)*.Dividing this distance by the mean of the distances.

Converting all infinite, no change (e.g., A->A), and NA distances to zero.

The 1-mer substitution matrix is transformed into a distance matrix by:

Symmetrize the 1-mer substitution matrix.

Converting the rates to distance

*d=-log10(p)*.Dividing this distance by the mean of the distances.

Converting all infinite, no change (e.g., A -> A), and NA distances to zero.

For input of TargetingModel, a matrix of distances for each 5-mer motif with rows names defining the center nucleotide and column names defining the 5-mer nucleotide sequence. For input of 1-mer substitution matrix, a 4x4 symmetric distance matrix.

See TargetingModel for this class of objects and createTargetingModel for building one.

1 2 3 4 5 | ```
# Calculate targeting distance of HH_S5F
dist <- calcTargetingDistance(HH_S5F)
# Calculate targeting distance of HH_S1F
dist <- calcTargetingDistance(HH_S1F)
``` |

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