Description Usage Arguments Value Examples
View source: R/util_functions.R
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.
1 2 | pairwise.jaccard(data, vp.pos, wSize = 21, qWd = 1.5, qWr = 1,
minDist = 15000)
|
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 |
a matrix containing the pairwise Jaccard similarity scores
1 2 | data <- readMultiple(f[1:3], vp.pos = 65923803)
res <- combined.analysis(data, num.exp=3, vp.pos = 65923803)
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