single.analysis: Single experiment 4C/Capture C analysis

In deWitLab/peakC: Perform peak calling for 4C/Capture-C experiments

Description

Function for identifying interaction peaks above a background distribution. A list containing a 4C/Capture-C dataset is required as input. The viewpoint position is given in the vp.pos argument.

Usage

single.analysis(data, vp.pos, wSize = 21, qWd = 1.5, qWr = 1,
  minDist = 15000)

Arguments

data	list containing the 4C/CapC data in two column format, an additional element num.exp describes the number of experiments
vp.pos	viewpoint position, this can be a single value or a two values to analyse a viewpoint region
wSize	number of fragments in a window
qWd	threshold for difference from the background
qWr	threshold for ratio over the background
minDist	minimal region around the viewpoint to exclude for the significance analysis
alphaFDR	false-discovery rate threshold

Value

a list containing a matrix with the data and the background model and a vector with the significant fragments

Examples

data <- readMultiple(f[1:3], vp.pos = 65923803)
res <- combined.analysis(data, num.exp=3, vp.pos = 65923803)

deWitLab/peakC documentation built on May 28, 2019, 7:53 p.m.