shazam (version 0.1.9)

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)

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.

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.

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

# NOT RUN {
# Calculate targeting distance of HH_S5F
dist <- calcTargetingDistance(HH_S5F)

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

# }