FisHiCal (version 1.1)

updateCalib: Update a parameter value in the calibration model

Description

A function to update a given parameter in the calibration model.

Usage

updateCalib(calib, paramVal, paramIndex)

Arguments

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.

paramVal

The new value of the parameter to be updated.

paramIndex

The index of the parameter to be updated in the parameter list of calib.

Value

An updated calibration model (an updated calib object).

Details

Users may want to refine the parameters of the calibration model. For example, in the model generated with prepareCalib the user may wish to increase the threshold value in order to discard less information in the calibration step.

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 calibrate match

Examples

 data(match) 
 npoints = 10 # number of points to fit
 
 # prepareCalib computes threshold according to the fit 
 # useMax is set to FALSE
 res = prepareCalib(match, npoints, useMax = FALSE)
 calib = res$calib
 calib
 calib = updateCalib(calib, 3.9, 3)
 calib