Introduction

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome conformation capture assays such as Hi-C as well as newer technologies such as PLAC-seq, HiChIP and region capture Hi-C. When using Fit-Hi-C with Hi-C data, we strongly suggest using bias values from matrix balancing-based normalization methods such as ICE or KR to control for experimental and techical biases in significance estimation. While using bias values, please make sure to use RAW counts and NOT the normalized counts as normalization will be taken into account through bias values. Here we provide an R implementation of Fit-Hi-C. Compared to its original implementation in Python (https://noble.gs.washington.edu/proj/fit-hi-c), Fit-Hi-C R port has the following advantages:

  • Fit-Hi-C R package is more efficient than Python original by re-writting some logic in C/C++
  • Fit-Hi-C R package is easy to use for those familiar with R language and Bioconductor without additional configuration
  • Bug fixes on “nan” errors in q-value computation and plotting
  • Compatible with output of hicpro2fithic.py script available in HiCPro 2.8.1

Install FitHiC

To install this package, start R and enter

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("FitHiC")

Example I: Yeast (S. cerevisiae) Hi-C data at single restriction enzyme (RE) resolution without bias values

Duan_yeast_EcoRI

FRAGSFILE and INTERSFILE are located in system.file("extdata", "fragmentLists/Duan_yeast_EcoRI.gz", package = "FitHiC") and system.file( "extdata", "contactCounts/Duan_yeast_EcoRI.gz", package = "FitHiC"), respectively. When input data is ready, run as follows:

library("FitHiC")
fragsfile <- system.file("extdata", "fragmentLists/Duan_yeast_EcoRI.gz",
    package = "FitHiC")
intersfile <- system.file("extdata", "contactCounts/Duan_yeast_EcoRI.gz",
    package = "FitHiC")
outdir <- file.path(getwd(), "Duan_yeast_EcoRI")
FitHiC(fragsfile, intersfile, outdir, libname="Duan_yeast_EcoRI",
    distUpThres=250000, distLowThres=10000)

Internally, Fit-Hi-C will successively call generate_FragPairs, read_ICE_biases, read_All_Interactions, calculateing_Probabilities, fit_Spline methods. The execution of Fit-Hi-C will be successfully completed till the following log appears:

## Fit-Hi-C is processing ...
## Running parse_Fragsfile method ...
## Complete parse_Fragsfile method [OK]
## Running parse_Intersfile method ...
## Complete parse_Intersfile method [OK]
## Running generate_FragPairs method ...
## Complete generate_FragPairs method [OK]
## Running read_All_Interactions method ...
## Complete read_All_Interactions method [OK]
## Running calculating_Probabilities method ...
## Writing Duan_yeast_EcoRI.fithic_pass1.txt
## Complete calculating_Probabilities method [OK]
## Running fit_Spline method ...
## Writing p-values to file Duan_yeast_EcoRI.spline_pass1.significances.txt.gz
## Complete fit_Spline method [OK]
## Running calculating_Probabilities method ...
## Writing Duan_yeast_EcoRI.fithic_pass2.txt
## Complete calculating_Probabilities method [OK]
## Running fit_Spline method ...
## Writing p-values to file Duan_yeast_EcoRI.spline_pass2.significances.txt.gz
## Complete fit_Spline method [OK]
## Execution of Fit-Hi-C completed successfully. [DONE]
## .Primitive("return")

The output files come from two internal methods called by Fit-Hi-C.

  • calculate_Probabilites
Duan_yeast_EcoRI.fithic_pass1.txt
avgGenomicDist contactProbability standardError noOfLocusPairs totalOfContactCounts
10105 3.12e-05 2.7e-06 322 22212
10315 3.05e-05 2.5e-06 330 22251
10545 2.87e-05 2.1e-06 350 22191
10779 2.97e-05 3.0e-06 344 22583
10982 3.16e-05 2.7e-06 323 22532
11196 3.32e-05 2.7e-06 302 22185
Duan_yeast_EcoRI.fithic_pass2.txt
avgGenomicDist contactProbability standardError noOfLocusPairs totalOfContactCounts
10107 1.15e-05 8e-07 252 6428
10317 1.31e-05 9e-07 266 7709
10546 1.43e-05 8e-07 281 8887
10779 1.27e-05 8e-07 285 7974
10982 1.32e-05 8e-07 255 7426
11196 1.40e-05 8e-07 238 7356
  • fit_Spline
Duan_yeast_EcoRI.spline_pass1.significances.txt.gz
chr1 fragmentMid1 chr2 fragmentMid2 contactCount p_value q_value
10 100894 10 150593 2 0.9988785 1
10 100894 10 162267 1 0.9985433 1
10 100894 10 169783 2 0.9708609 1
10 100894 10 179515 3 0.8072602 1
10 100894 10 182528 1 0.9831568 1
10 100894 10 185071 1 0.9795001 1
Duan_yeast_EcoRI.spline_pass2.significances.txt.gz
chr1 fragmentMid1 chr2 fragmentMid2 contactCount p_value q_value
10 100894 10 150593 2 0.9813195 1
10 100894 10 162267 1 0.9902851 1
10 100894 10 169783 2 0.8983241 1
10 100894 10 179515 3 0.6547083 1
10 100894 10 182528 1 0.9571117 1
10 100894 10 185071 1 0.9501637 1

If visual is set to TRUE, corresponding images will be also outputed: