calculateFingerprintMap {Scale4C} | R Documentation

## Calculate scale-space fingerprint map for given 4C-seq data

### Description

`calculateFingerprintMap` uses the scale space map to calculate the inflection points of the smoothed signals.

### Usage

    calculateFingerprintMap(data, maxSQSigma = 5000, epsilon = 0.0000001)

### Arguments

`data` | Scale-space object for the 4C-seq data
`maxSQSigma` | Maximum square sigma used to calculate the fingerprint map
`epsilon` | Small numeric value (can also be zero); used to test for inflection points

### Details

Scale4C uses Gauss kernels of increasing (square) sigma to smooth the original 4C-seq signal. The resulting inflection points for a chosen sigma are stored in the corresponding line of the fingerprint map, i.e. a 2D matrix (position x sigma).

### Value

A Scale4C object containing the fingerprint map for a Scale4C object, i.e. a matrix with quite a lot of zeros and the occasional 2 or -1 as symbols for inflection points. The fingerprint map is included as second assay of the Scale4C object's scaleSpace SummarizedExperiment slot.

### Author(s)

Carolin Walter

### Examples

        # read prepared example data
        data(liverData)
        # use small maxSQSigma for a fast example
        liverData<-calculateFingerprintMap(liverData, maxSQSigma = 50)
        head(t(assay(scaleSpace(liverData), 2))[1:10,1:20])

[Package Scale4C version 1.16.0 Index]