getInfoLevelForChr:
Compute the information level for a given chromosome after calibration
Description
A function to compute the information proportions in a a given calibrated Hi-C matrix for a given chromosome. This will be the proportions of non-zero cells, representing information that was not discarded in the calibration step.
Usage
getInfoLevelForChr(calibHiC, hicCoord, chr)
Arguments
calibHiC
A calibrated Hi-C matrix. This matrix could be prepared with calibrate.
hicCoord
The genomic coordinates of the Hi-C bins. A data frame with the following mandatory columns: chr (chromosome name), start (start position), end (end position). Additional columns are permitted but will not be used.
chr
The name of the chromosome of interest (as it appears in hicCoord).
Value
The information level for the given chromosome in the calibrated Hi-C matrix.
Details
The level of information can affect the accuracy of the 3D prediction, which may be lower for sparse calibration matrices (information level < 0.4).
References
Y. Shavit, F.K. Hamey, P. Lio', FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, 2014 (submitted).