spotgear_identifyMajorPeaks: Identify peaks based on the ridges in 2-D CWT coefficient...

Description Usage Arguments Value

Description

Indentify the peaks based on the ridge list (returned by getRidge) in 2-D CWT coefficient matrix and estimated Signal to Noise Ratio (SNR)

Usage

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spotgear_identifyMajorPeaks(ms, ridgeList, wCoefs,
  scales = as.numeric(colnames(wCoefs)), SNR.Th = 3,
  peakScaleRange = c(5, 64), ridgeLength = 32, nearbyPeak = TRUE,
  nearbyWinSize = 100, winSize.noise = 10, SNR.method = "quantile",
  minNoiseLevel = 0.001, shape_ratio = 0.01, minPeakArea = 0.05)

Arguments

ms

The autoradiointensity data

ridgeList

Returned by getRidge

wCoefs

2-D CWT coefficients

scales

The scales of the wavelet function to be matched to the signal. Scales of CWT, by default it is the colnames of wCoefs

SNR.Th

Threshold of SNR

peakScaleRange

The CWT scale range of the peak.

ridgeLength

The maximum ridge scale of the major peaks.

nearbyPeak

Determine whether to include the small peaks close to large major peaks

nearbyWinSize

The window size to determine the nearby peaks. Only effective when nearbyPeak is true.

winSize.noise

The local window size to estimate the noise level.

SNR.method

Method to estimate noise level. Currently, only 95 percentage quantile is supported.

minNoiseLevel

The minimum noise level used in calculating SNR, i.e., if the estimated noise level is less than "minNoiseLevel", it will use "minNoiseLevel" instead. If the noise level is less than 0.5, it will be treated as the ratio to the maximum amplitude of the spectrum.

shape_ratio

A peak should have peak area at least shape_ratio of the maximum one. Because the same sample could be run on multiple gels with different exposure lengths, we pick peaks relative to the maximum peak values (using shape_ratio).

minPeakArea

The minimum area for a peak if to call a location a peak. An important peak should have non-ignorable peak area

Value

Return a list with following elements:

All of these return elements have peak names, which are the same as the corresponding peak ridges. see getRidge for details.


oslerinhealth/spotgear documentation built on May 25, 2021, 10:38 p.m.