waveletThresholding: Perform Wavelet CWT Thresholding

In WaveSeqR: A Wavelet-based Method for ChIP-Seq peak calling

Description

Apply precomputed wavelet coefficient threshold to continuous wavelet transform (CWT) of specified input data. Thresholding performed chromosome-by-chromosome. Only scales > minscale considered for peak detection. Number of significant scales has to be > minsig for the window to be considered significant.

Usage

waveletThresholding(infile, outdir, exptname, mother = "morlet", winsize = 200, minsig = 2, minsigscale = 3, 
	maxsigscale = -1, p.thres = 0.2, p.min = 0.001, p.max = 0.3)

Arguments

infile	Input padded graph file (required)
outdir	Output directory (required)
exptname	Unique string to identify name of experiment (required)
mother	Wavelet mother function used for the CWT. Tested choices are "morlet","haar","gaussian1", "gaussian2" (default="morlet")
winsize	Window size for padded graph files (default=200)
minsig	Minimum number of significant scales for a window to be considered significant (default=2)
minsigscale	Minimum significant scale considered for peak detection (default=3)
maxsigscale	Minimum significant scale considered for peak detection (default=-1)
p.thres	Threshold p-value for calling significant windows (default=0.2)
p.min	Minimum quantile (1-p.min) to be output for wavelet coefficient distribution (default=0.3)
p.max	Maximum quantile (1-p.max) as above (default=0.001)

Details

This function writes the results from the wavelet thresholding into a file within the peaks folder of outdir.

Note

Function messages are piped to a log file which can be found in the log folder of outdir.

Author(s)

Apratim Mitra

See Also

wavCWT

WaveSeqR documentation built on May 2, 2019, 5:19 p.m.