Description Usage Arguments Value Author(s) References See Also Examples
A function for applying a calibration function to a given Hi-C contact matrix.
1 |
hic |
A numeric matrix/vector of pairwise Hi-C contact frequencies. |
calib |
A list with f, the calibration function, and params a list of parameters for f.
This object can be generated with the function |
A calibrated version of the input matrix (or vector), i.e. the result of applying the calibration function (f) on the values of 'hic'. Zero values represent discarded/missing information.
Yoli Shavit
Y. Shavit, F.K. Hamey, P. Lio', FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, 2014 (submitted).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | data(match)
data(hic)
npoints = 10 # number of points to fit
# prepareCalib computes threshold to fit
res = prepareCalib(match, npoints, useMax = FALSE)
calib = res$calib
calib$f # calibration function
calib$params # the parametrs for f
# note that calib could be refined by the user
# now calibrate the hic matrix
calibHiC = calibrate(hic, calib)
plot(match$distances, calibHiC[upper.tri(calibHiC)],
xlab = "distances", ylab = "calibrated distances")
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