gapDiagnostic: Function to Select Suitable Gap Size

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

Description

Calculates and plots fraction of total reads in topN peaks for a specified range of gap sizes.

Usage

gapDiagnostic(peaks, gap.max = 15, topN = 10000, winsize = 200, plot.flag = TRUE)

Arguments

peaks	data.frame or file containing list of peaks output by WaveSeqR.
gap.max	Maximum gap size for the gap diagnostic calculation (default = 15).
topN	Number of peaks to perform above calculation (default=1000). Should be adjusted to equal the maximum number of expected peaks.
winsize	Window size used for peak-calling and bedGraph files.
plot.flag	If TRUE, plots the gap diagnostic curve.

Value

Returns a vector of length gap.max + 1 with fraction of total reads in topN peaks for gap sizes ranging from 0 to gap.max.

Author(s)

Apratim Mitra

See Also

gapPeaks

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

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