# Iterative FISH-based Calibration of Hi-C Data

## Documentation for package ‘FisHiCal’ version 1.1

- DESCRIPTION file.

## Help Pages

FisHiCal-package | Iterative FISH-based Calibration of Hi-C Data
calibHiC | in-silico 100*100 calibrated Hi-C contact matrix
calibrate | Hi-C calibration
conf | A 3D random configuration of 100 points
findMatchingIndices | Find matching Hi-C bins for FISH probes, using mid-points
FisHiCal | Iterative FISH-based Calibration of Hi-C Data
getInfoLevelForChr | Compute the information level for a given chromosome after calibration
hic | in-silico 100*100 Hi-C contact matrix with with 5% noise
lsmacof | 3D reconstruction from Hi-C distances
match | in-silico FISH distances and matching Hi-C frequencies with 5% noise
plotInc | Plot a spatial inconsistency
prepareCalib | Prepare Hi-C calibration
prepareData | Match FISH distances and Hi-C frequencies for calibration
searchInc | Search for spatial inconsistencies
spatialInc | Spatial inconsistencies detected for loci in fibroblasts chromosome 1
summaryInc | Summarize spatial inconsistencies.
updateCalib | Update a parameter value in the calibration model