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:
To install this package, start R and enter
## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("FitHiC")
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.
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 |
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 |
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 |
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:
Duan_yeast_HindIII
Similarly, Duan_yeast_HindIII can be run as follows:
library("FitHiC")
fragsfile <- system.file("extdata",
"fragmentLists/Dixon_hESC_HindIII_hg18_w40000_chr1.gz",
package = "FitHiC")
intersfile <- system.file("extdata",
"contactCounts/Dixon_hESC_HindIII_hg18_w40000_chr1.gz",
package = "FitHiC")
outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_w40000_chr1")
FitHiC(fragsfile, intersfile, outdir,
libname="Dixon_hESC_HindIII_hg18_w40000_chr1", noOfBins=50,
distUpThres=5000000, distLowThres=50000, visual=TRUE)