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

In walter-ca/Scale4C: Scale4C: an R/Bioconductor package for scale-space transformation of 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])

walter-ca/Scale4C documentation built on May 5, 2019, 9:03 p.m.