Iterative FISH-based Calibration of Hi-C Data

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Documentation for package ‘FisHiCal’ version 1.1

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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