pairwise.jaccard: Single experiment Jaccard similarity calculation

Description Usage Arguments Value Examples

View source: R/util_functions.R

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

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pairwise.jaccard(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 matrix containing the pairwise Jaccard similarity scores

Examples

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

deWitLab/peakC documentation built on May 6, 2018, 8:50 p.m.