FisHiCal (version 1.1)

calibrate: Hi-C calibration

Description

A function for applying a calibration function to a given Hi-C contact matrix.

Usage

calibrate(hic, calib)

Arguments

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 prepareCalib.

Value

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.

References

Y. Shavit, F.K. Hamey, P. Lio', FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, 2014 (submitted).

See Also

prepareCalib conf hic match

Examples

 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")