getThresholdDistribution: Wavelet Threshold Estimation

Description Usage Arguments Details Warning Note Author(s) See Also

View source: R/getThresholdDistribution.R

Description

Obtains wavelet coefficient distributions for the specified input file using the continuous wavelet transform (CWT). Monte Carlo sampling is performed with N samples of size 2^maxscale and coefficients are obtained at a range of quantiles defined by the range [1-p.min,1-p.max]. Statified sampling is performed chromosome-by-chromosome weighted by chromosome length.

Usage

1
getThresholdDistribution(infile, outdir, exptname, mother = "morlet", N = 5000, maxscale = 12, 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")

N

Number of samples (default=5000)

maxscale

Maximum scale of wavelet decomposition. Also defines size of sample (2^maxscale) (default=12)

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 outputs wavelet coefficient thresholds in increments of p.max for each chromosome to the thresdist folder of outdir.

Warning

For large values of N and small values of winsize this step can be time-consuming.

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.