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 | combined.analysis(data, num.exp = 0, vp.pos, wSize = 21, alphaFDR = 0.1,
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 |
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 |
a list containing a matrix with the data and the background model and a vector with the significant fragments
1 2 | data <- readMultiple(f[1:3], vp.pos = 65923803)
res <- combined.analysis(data, num.exp=3, vp.pos = 65923803)
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