HiContacts

Workflows

Standard Workflow

library(HiCExperiment)
library(HiContacts)
library(HiContactsData)

# Import Hi-C matrix
cool_file <- HiContactsData('yeast_wt', format = 'cool')
hic <- import(cool_file, format = 'cool')

# Perform matrix arithmetic
hic_detrended <- detrend(hic)
hic_smooth <- despeckle(hic)

# Plot contact map
plotMatrix(hic_smooth, use.scores = 'balanced.despeckled')

Input: A HiCExperiment object. Output: Detrended, smoothed, or merged contact maps and their corresponding plots.

Contact Map Analysis

library(HiCExperiment)
library(HiContacts)
library(HiContactsData)

mcool_file <- HiContactsData('yeast_wt', format = 'mcool')
hic <- import(mcool_file, format = 'mcool', resolution = 1000)

# Calculate cis-trans ratios
ratios <- cisTransRatio(hic)

# Compute distance decay P(s) curves
ps <- distanceLaw(hic)

Input: A HiCExperiment object, optionally with an associated pairs file. Output: A tibble of cis-trans ratios and distance decay P(s) curves.

Topological Feature Mapping

library(HiCExperiment)
library(HiContacts)
library(HiContactsData)

mcool_file <- HiContactsData('yeast_wt', format = 'mcool')
hic <- import(mcool_file, format = 'mcool', resolution = 16000)

# Map chromosome compartments
hic <- getCompartments(hic, chromosomes = c('XV', 'XVI'))

# Compute insulation scores and borders
hic <- refocus(hic, 'II:1-300000') |> 
    zoom(resolution = 1000) |> 
    getDiamondInsulation(window_size = 8000) |> 
    getBorders()

Input: A HiCExperiment object. Output: A HiCExperiment object updated with compartments, insulation scores, and domain borders.

When to Use

• Visualizing Hi-C contact matrices as heatmaps (square or horizontal) using plotMatrix().
• Performing matrix arithmetic such as detrending (detrend()), autocorrelating (autocorrelate()), merging (merge()), dividing (divide()), and smoothing (despeckle()).
• Mapping chromosome compartments (getCompartments()), insulation scores (getDiamondInsulation()), and domain borders (getBorders()).
• Analyzing distance decay curves using distanceLaw() and plotting them with plotPs() or plotPsSlope().

When NOT to Use

• For initial raw sequence alignment or filtering of fastq files, use pipelines like HiC-Pro, distiller, or Juicer instead of HiContacts.
• For general genomic interval manipulation without interaction data, use GenomicRanges or IRanges directly.

Data Requirements

• A HiCExperiment object imported from .cool, .mcool, .hic, or HiC-Pro files.
• For accurate distance decay P(s) curves, an associated pairs file (e.g., .pairs.gz) should be linked using pairsFile(hic) <- ....

Key Parameters

• use.scores ('balanced'): Specifies which interaction score type to plot or analyze (e.g., 'balanced', 'detrended', 'autocorrelated').
• limits (NULL): A numeric vector of length 2 specifying the color scale limits in plotMatrix().
• maxDistance (NULL): Maximum distance from the diagonal to plot in horizontal matrices.
• focal.size (5): Size of the focal window used for smoothing in despeckle().
• window_size (8000): Window size in base pairs for computing diamond insulation scores in getDiamondInsulation().
• chromosomes (NULL): Vector of chromosome names to restrict compartment calling in getCompartments().

Best Practices

• Always use normalized scores (like 'balanced') rather than raw counts for comparative analyses.
• Link a physical pairs file using pairsFile() before running distanceLaw() to avoid approximations in the P(s) curve.
• Export computed topological features (e.g., compartments or insulation scores) to standard formats like BigWig or BED using rtracklayer::export().

Common Pitfalls

• Running distanceLaw() without a pairs file: This results in an approximation warning. Fix by assigning a pairs file to the HiCExperiment object first.
• Plotting matrices with extreme dynamic ranges without log transformation: Use scale = 'log10' in plotMatrix() to improve visualization.

Alternatives

• diffHic: For differential analysis of Hi-C data using biological replicates.

Citations

• Serizay J, Matthey-Doret C, Bignaud A, Baudry L, Koszul R (2024). "Orchestrating chromosome conformation capture analysis with Bioconductor." Nature Communications, 15, 1-9. doi:10.1038/s41467-024-44761-x.

References

• Homepage: bioconductor.org/packages/HiContacts
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/HiContacts/inst/doc/HiContacts.html