shazam (version 1.2.0)

calcTargetingDistance: Calculates a 5-mer distance matrix from a TargetingModel object

Description

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.

Usage

calcTargetingDistance(model, places = 2)

Value

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.

Arguments

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.

Details

The targeting model is transformed into a distance matrix by:

1. Converting the likelihood of being mutated \(p=mutability*substitution\) to distance \(d=-log10(p)\).

2. Dividing this distance by the mean of the distances.

3. 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:

1. Symmetrize the 1-mer substitution matrix.

2. Converting the rates to distance \(d=-log10(p)\).

3. Dividing this distance by the mean of the distances.

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

See Also

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

Examples

# Calculate targeting distance of HH_S5F
dist <- calcTargetingDistance(HH_S5F)

# Calculate targeting distance of HH_S1F
dist <- calcTargetingDistance(HH_S1F)