combined.analysis: Combined 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 of 4C/Capture-C datasets are required as input. The viewpoint position is given in the vp.pos argument.

Usage

combined.analysis(data, num.exp = 0, vp.pos, wSize = 21, alphaFDR = 0.1,
  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
num.exp	number of experiments, used in conjuction with "data" and "multi" in type, default is 0 which means the number in the data list is used, a different number overwrites the default number
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
alphaFDR	false-discovery rate threshold
minDist	minimal region around the viewpoint to exclude for the significance analysis
qW	threshold for absolute difference

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.