# `HiCcompare` Vignette

# Introduction

`HiCcompare` provides functions for the joint normalization and detection of differential chromatin interactions between two or multiple Hi-C datasets. `HiCcompare` operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format (see Creating the hic.table object). Functions to convert popular Hi-C data formats (`.hic`, `.cool`) to sparse format are available (see ?cooler2sparse). `HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust permutation method for detecting differences between Hi-C datasets.

The `hic_loess` function outputs normalized chromatin interactions for both matrices ready for the comparative analysis. The `hic_compare` function performs the comparative analysis and outputs genomic coordinates of pairs of regions detected as differentially interacting, interaction frequencies, the difference and the corresponding permutation p-value.

# How to use `HiCcompare`

## Installation

Install `HiCcompare` from Bioconductor.

    if (!requireNamespace("BiocManager", quietly=TRUE))
        install.packages("BiocManager")
    BiocManager::install("HiCcompare")
    library(HiCcompare)

## Getting Hi-C Data

You will need processed Hi-C data in the form of sparse upper triangular matrices or BEDPE files in order to use `HiCcompare`. Data is available from several sources and two examples for downloading and extracting data are listed below. If you have full Hi-C contact matrices you can convert them to sparse upper triangular format using the full `full2sparse` function as shown in additional functions

### Extracting data from `.hic` files

Hi-C data is available from several sources and in many formats. `HiCcompare` is built to work with the sparse upper triangular matrix format popularized by the lab of Erez Lieberman-Aiden http://aidenlab.org/data.html. If you already have Hi-C data either in the form of a sparse upper triangular matrix or a full contact matrix you can skip to the Creating the hic.table object section. If you obtain data from the Aiden Lab in the `.hic` format you will need to first extract the matrices that you wish to compare.

1. Download the `straw` software from https://github.com/theaidenlab/straw/wiki and install it.
2. Use `straw` to extract a Hi-C sparse upper triangular matrix. An example is below:

Say we downloaded the `GSE63525_K562_combined_30.hic` file from GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525

To extract the raw matrix corresponding to chromosome 22 at 500kb resolution we would use the following command within the terminal

`./straw NONE GSE63525_K562_combined_30.hic 22 22 BP 500000 > K562.chr22.500kb.txt`

This will extract the matrix from the `.hic` file and save it to the `K562.chr22.500kb.txt` text file, in the sparse upper triangular matrix format. See more examples on on how to use `straw` at https://github.com/theaidenlab/straw/wiki/CPP#running. Straw requires several inputs for the extraction of data from a `.hic` file.

`<NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize>`

The first argument is the normalization method. For use in `HiCcompare` you want the raw data so you should selected `NONE`. The second argument is the `.hic` file name. Next is the chromosome numbers of the matrix you want. For an intrachromosomal contact map both should be the same as in the above example. If you want a matrix of interchromosomal interactions you can use different chromosomes i.e. interactions between chromosome 1 and chromosome 2 (Note that `HiCcompare` is only meant to be used on intrachromosomal interactions at this point in development). The next argument is whether you want basepair or fragment files. For `HiCcompare` use `BP`. The final argument is the binsize of the matrix (the resolution). To extract a matrix at a resolution of 1MB enter `10000000`. Typical bin sizes are 1MB, 500KB, 100KB, 50KB, 5KB, 1KB. Note that most matrices with resolutions higher than 100KB (i.e. matrices with resolutions of 1KB - 50KB) are typically too sparse (due to insufficient sequencing coverage) for analysis in `HiCcompare`.

From here we can just import the matrix into R as you would normally for any tab-delimited file.

3. Import the data into R `K562.chr22 <- read.table('K562.chr22.500kb.txt', header=FALSE)`
4. Repeat these steps for any other Hi-C dataset that you wish to compare to the first dataset using `HiCcompare`, then proceed to Creating the `hic.table` object.

### Extracting data from `.cool` files

The `cooler` software, http://cooler.readthedocs.io/en/latest/index.html, allows access to a large collection of Hi-C data. The cooler index ftp://cooler.csail.mit.edu/coolers contains Hi-C data for `hg19` and `mm9` from many different sources.

`.cool` files can be read directly into R using the `cooler2bedpe` function provided by `HiCcompare`.

    dat <- cooler2bedpe(path = "Dixon2012-H1hESC-HindIII-allreps-filtered.1000kb.cool")

Alternatively, data in the `.cool` format can be import into `HiCcompare` using the following steps:

1. Download and install `cooler` from http://cooler.readthedocs.io/en/latest/index.html
2. Download the `GSM5981806_HiC_UT242.cool` file from GEO GSE199695.
3. See `cooler dump --help` for data extraction options. To extract the contact matrix we use the following commands in the terminal:
   `cooler dump --join GSM5981806_HiC_UT242.cool > GSM5981806_HiC_UT242.txt`
4. Read in the text file as you would any tab-delimited file in R
   `UT242 <- read.table(fileNameIn1, header = FALSE)`. Subset for speed, `UT242 <- UT242[UT242$V1 == "chr2" & UT242$V4 == "chr2", ]`
5. Convert to a sparse upper triangular matrix using the `HiCcompare::cooler2sparse` function.
   `sparse <- cooler2sparse(UT242)`
6. Repeat the steps for another Hi-C dataset that you wish to compare to the first dataset then proceed to Creating the `hic.table` object.

### Using data from HiC-Pro

HiC-Pro is another tool for processing raw Hi-C data into usable matrix files. HiC-Pro will produce a `.matrix` file and a `.bed` file for the data. These `.matrix` files are in sparse upper triangular format similar to the results of Juicer and the dumped contents of a `.hic` file, however instead of using the genomic start coordinates for the first two columns of the sparse matrix they use an ID number. The `.bed` file contains the mappings for each of these IDs to their genomic coordinates. `HiCcompare` includes a function to convert the results of HiC-Pro into a usable format for analysis in `HiCcompare`. When using data from HiC-Pro it is important to use the raw `.matrix` files and NOT the iced `.matrix` files. The iced `.matrix` files have already had ICE normalization applied to them and are not suitable for entry into `HiCcompare`. Here we convert HiC-Pro data for input into HiCcompare:

    # read in files
    mat <- read.table("hic_1000000.matrix")
    bed <- read.table("hic_1000000_abs.bed")
    # convert to BEDPE
    dat <- hicpro2bedpe(mat, bed)
    # NOTE: hicpro2bedpe returns a list of lists. The first list, dat$cis, contains the intrachromosomal contact matrices
    # NOTE: dat$trans contains the interchromosomal contact matrix which is not used in HiCcompare.

See the help using `?hicpro2bedpe` for more details.

## Detecting Copy Number Variations and Excluding regions

Before you start a `HiCcompare` analysis, you may want to detect CNV and exclude these regions along with any other regions known to exhibit changes or undesirable sequencing characteristics which could cause false positives. `HiCcompare` provides a function to perform a CNV detection analysis utilizing the `QDNAseq` R package. You will need to have your Hi-C data in `.bam` files. This can be accomplished by downloading the raw sequencing results and aligning them using one of the many Hi-C processing pipelines. Once you have `.bam` files place them in a specified folder and you can then run `get_CNV`. Make sure to specify the bin size you will be using in kilobase pairs. The bin size should be the same as the resolution of the Hi-C data that will be used in the `HiCcompare` analysis. The `CNV.level` option will allow you to choose which level of CNV you would like to exclude. The CNV calls are defined as -2 = deletion, -1 = loss, 0 = normal, 1 = gain, 2 = amplification. In order to exclude amplifications and deletions set `CNV.level = 2`. To exclude any amount of CNV set `CNV.level = 1`.

    cnv <- get_CNV(path2bam = 'path/to/bamfiles', out.file = 'path/to/bamfiles/outfile',
                   bin.size = 1000, genome = 'hg19', CNV.level = 2)

This function will run the CNV detection steps provided in `QDNAseq` and export a `.txt` file containing the copy number calls and a `.bed` file containing the regions detected at or above the chosen CNV level. It will also return a data.frame containing the regions at or above the chosen CNV level. It is recommended to exclude regions with scores of -2 or 2, however this decision is left up to the user.

You may want to exclude the regions with CNV along with blacklisted regions from any further analysis. `HiCcompare` has the ENCODE blacklists for hg19 and hg38 included (available using `data("hg19_blacklist")` or `data("hg38_blacklist")`). We can now create a data.frame (or `GenomicRanges` object) containing all of the regions we want to exclude from any further analysis.

    data('hg19_blacklist')

    # combine cnv excluded regions with blacklist regions
    exclude <- cbind(cnv, hg19_blacklist)

Now that we have a data.frame containing the regions to be excluded we just simply set the `exclude.regions` options in the `create.hic.table` function to the `exclude` data.frame.

## Creating the `hic.table` object

### Sparse upper triangular format

A sparse matrix format represents a relatively compact and human-readable way to store pair-wise interactions. It is a tab-delimited text format containing three columns: “region1” - a start coordinate (in bp) of the first region, “region2” a start coordinate of the second region, and “IF” - the interaction frequency between them (IFs). Zero IFs are dropped (hence, the sparse format). Since the full matrix of chromatin interactions is symmetric, only the upper triangular portion, including the diagonal, is stored.

If you have two full Hi-C contact matrices you can convert them to sparse upper triangular matrices using the `HiCcompare::full2sparse` function. Once you have two sparse matrices you are ready to create a `hic.table` object. This will be illustrated using the included sparse matrices at 500kb resolution for chromosome 22 from the HMEC and NHEK cell lines.

    library(`HiCcompare`)
    # load the data
    data("HMEC.chr22")
    data("NHEK.chr22")
    head(HMEC.chr22)

    ##    region1  region2   IF
    ## 1 16000000 16000000    5
    ## 2 16000000 16500000    2
    ## 3 16500000 16500000  297
    ## 4 16000000 17000000    5
    ## 5 16500000 17000000   92
    ## 6 17000000 17000000 5690

Now that we have 2 sparse upper triangular matrices we can create the `hic.table` object. `create.hic.table` requires the input of 2 sparse matrices and the chromosome name.

    # create the `hic.table` object
    chr22.table <- create.hic.table(HMEC.chr22, NHEK.chr22, chr = 'chr22')
    head(chr22.table)

    ##      chr1   start1     end1   chr2   start2     end2   IF1         IF2     D          M
    ##    <char>    <int>    <int> <char>    <int>    <int> <num>       <num> <num>      <num>
    ## 1:  chr22 16000000 16500000  chr22 16000000 16500000     5    5.203323     0 0.05750528
    ## 2:  chr22 16000000 16500000  chr22 16500000 17000000     2    8.672206     1 2.11639897
    ## 3:  chr22 16500000 17000000  chr22 16500000 17000000   297  480.440193     0 0.69389392
    ## 4:  chr22 16000000 16500000  chr22 17000000 17500000     5   14.742750     2 1.56000562
    ## 5:  chr22 16500000 17000000  chr22 17000000 17500000    92  277.510581     1 1.59283701
    ## 6:  chr22 17000000 17500000  chr22 17000000 17500000  5690 9435.359752     0 0.72964887

By default, all regions for the data entered are used as is. It may be desirable to exclude certain regions from any further analysis because they contain CNV or are overlapping blacklisted regions with known sequencing issues. To exclude the CNV and blacklisted regions we defined above, create the `hic.table` object as follows.

    chr22.table <- create.hic.table(HMEC.chr22, NHEK.chr22, chr = 'chr22', exclude.regions = exclude, exclude.overlap = 0.2)

The `exclude.overlap` option controls the percentage overlap required with the regions listed in your data in order to be exclude. CNV regions should in the same resolution and bins as your data so they will overlap any of your regions by 100%. Blacklisted regions tend to be small and may only overlap your regions by a few basepairs. If you want any amount of overlap to result in exclusion set `exclude.overlap = 0`. To require 100% overlap before exclusion set `exclude.overlap = 1`. By default this option will exclude regions with 20% or more overlap.

We can also list multiple `hic.tables` in order to utilize parallel computing. First we create another `hic.table` as was done above. Then we combine these two `hic.tables` into a list.

    # create list of `hic.table` objects
    data("HMEC.chr10")
    data("NHEK.chr10")

    # create the `hic.table` object
    chr10.table <- create.hic.table(HMEC.chr10, NHEK.chr10, chr = 'chr10')
    hic.list <- list(chr10.table, chr22.table)
    head(hic.list)

    ## [[1]]
    ##          chr1    start1      end1   chr2    start2      end2   IF1          IF2     D          M
    ##        <char>     <int>     <int> <char>     <int>     <int> <num>        <num> <num>      <num>
    ##     1:  chr10         0    500000  chr10         0    500000 11160 1.491828e+04     0  0.4187441
    ##     2:  chr10         0    500000  chr10    500000   1000000  3339 4.766792e+03     1  0.5136024
    ##     3:  chr10    500000   1000000  chr10    500000   1000000 15871 1.998235e+04     0  0.3323333
    ##     4:  chr10         0    500000  chr10   1000000   1500000  1064 6.501731e+02     2 -0.7106025
    ##     5:  chr10    500000   1000000  chr10   1000000   1500000  2963 2.097443e+03     1 -0.4984269
    ##    ---
    ## 35366:  chr10 134000000 134500000  chr10 135000000 135500000  1810 1.273570e+03     2 -0.5071112
    ## 35367:  chr10 134500000 135000000  chr10 135000000 135500000  1971 3.634653e+03     1  0.8828898
    ## 35368:  chr10 135000000 135500000  chr10 135000000 135500000 16716 1.188368e+04     0 -0.4922479
    ## 35369:  chr10 134000000 134500000  chr10 135500000 136000000     1 6.865608e-01     3 -0.5425406
    ## 35370:  chr10 135000000 135500000  chr10 135500000 136000000     4 3.432804e+00     1 -0.2206125
    ##
    ## [[2]]
    ##         chr1   start1     end1   chr2   start2     end2   IF1         IF2     D           M
    ##       <char>    <int>    <int> <char>    <int>    <int> <num>       <num> <num>       <num>
    ##    1:  chr22 16000000 16500000  chr22 16000000 16500000     5    5.203323     0  0.05750528
    ##    2:  chr22 16000000 16500000  chr22 16500000 17000000     2    8.672206     1  2.11639897
    ##    3:  chr22 16500000 17000000  chr22 16500000 17000000   297  480.440193     0  0.69389392
    ##    4:  chr22 16000000 16500000  chr22 17000000 17500000     5   14.742750     2  1.56000562
    ##    5:  chr22 16500000 17000000  chr22 17000000 17500000    92  277.510581     1  1.59283701
    ##   ---
    ## 2479:  chr22 49000000 49500000  chr22 51000000 51500000    21   54.634896     4  1.37943338
    ## 2480:  chr22 49500000 50000000  chr22 51000000 51500000    35   71.112086     3  1.02273986
    ## 2481:  chr22 50000000 50500000  chr22 51000000 51500000   394  339.083241     2 -0.21655615
    ## 2482:  chr22 50500000 51000000  chr22 51000000 51500000  4066 2741.284207     1 -0.56875831
    ## 2483:  chr22 51000000 51500000  chr22 51000000 51500000  9916 7132.021930     0 -0.47544713

The `hic.table` object contains a summary of the differences between the two matrices. “IF1” and “IF2” correspond to interaction frequencies in the first and second matrices, “D” is the unit distance (length of each unit is equivalent to the resolution of the data, e.g., 500kb), “M” is the \(log_2(IF2)-log_2(IF1)\) difference.

### BEDPE format

A `hic.table` object can also be created using data in the 7 column BEDPE format. An example of BEDPE data for the HMEC dataset used above is shown below.

    ##      chr1   start1     end1   chr2   start2     end2   IF1
    ##    <char>    <int>    <int> <char>    <int>    <int> <num>
    ## 1:  chr22 16000000 16500000  chr22 16000000 16500000     5
    ## 2:  chr22 16000000 16500000  chr22 16500000 17000000     2
    ## 3:  chr22 16500000 17000000  chr22 16500000 17000000   297
    ## 4:  chr22 16000000 16500000  chr22 17000000 17500000     5
    ## 5:  chr22 16500000 17000000  chr22 17000000 17500000    92
    ## 6:  chr22 17000000 17500000  chr22 17000000 17500000  5690

To create a `hic.table` object using BEDPE data is very similar to using data in the sparse upper triangular format.

    bed.hic.tab <- create.hic.table(HMEC.chr22_BEDPE, NHEK.chr22_BEDPE)
    head(bed.hic.tab)

    ##      chr1   start1     end1   chr2   start2     end2   IF1         IF2     D          M
    ##    <char>    <int>    <int> <char>    <int>    <int> <num>       <num> <num>      <num>
    ## 1:  chr22 16000000 16500000  chr22 16000000 16500000     5    5.203323     0 0.05750528
    ## 2:  chr22 16000000 16500000  chr22 16500000 17000000     2    8.672206     1 2.11639897
    ## 3:  chr22 16500000 17000000  chr22 16500000 17000000   297  480.440193     0 0.69389392
    ## 4:  chr22 16000000 16500000  chr22 17000000 17500000     5   14.742750     2 1.56000562
    ## 5:  chr22 16500000 17000000  chr22 17000000 17500000    92  277.510581     1 1.59283701
    ## 6:  chr22 17000000 17500000  chr22 17000000 17500000  5690 9435.359752     0 0.72964887

### HiC-Pro format

If you are using data from HiC-Pro you can create a `hic.table` object as follows.

    # first dataset
    mat1 <- read.table("hic1_1000000.matrix")
    bed1 <- read.table("hic1_1000000_abs.bed")
    dat1 <- hicpro2bedpe(mat, bed)
    dat1 <- dat1$cis # extract intrachromosomal matrices
    # second dataset
    mat2 <- read.table("hic2_1000000.matrix")
    bed2 <- read.table("hic2_1000000_abs.bed")
    dat2 <- hicpro2bedpe(mat, bed)
    dat2 <- dat2$cis # extract intrachromosomal matrices

    # for chr1
    hic.table <- create.hic.table(dat1[[1]], dat2[[1]])

    # for all chromosomes
    hic.list <- mapply(create.hic.table, dat1, dat2, SIMPLIFY = FALSE)

### InteractionSet/GRanges format

A `hic.table` can also be created using an `InteractionSet` object. Simply enter two `InteractionSets` representing two Hi-C matrices into the `create.hic.table` function and they will be converted to the proper format. See the `InteractionSet` vignette for creating `InteractionSet` objects here

    data("hmec.IS")
    data("nhek.IS")
    head(hmec.IS)

    ## GInteractions object with 6 interactions and 1 metadata column:
    ##       seqnames1           ranges1     seqnames2           ranges2 |        IF
    ##           <Rle>         <IRanges>         <Rle>         <IRanges> | <numeric>
    ##   [1]     chr22 16000000-16499999 ---     chr22 16000000-16499999 |         5
    ##   [2]     chr22 16000000-16499999 ---     chr22 16500000-16999999 |         2
    ##   [3]     chr22 16500000-16999999 ---     chr22 16500000-16999999 |       297
    ##   [4]     chr22 16000000-16499999 ---     chr22 17000000-17499999 |         5
    ##   [5]     chr22 16500000-16999999 ---     chr22 17000000-17499999 |        92
    ##   [6]     chr22 17000000-17499999 ---     chr22 17000000-17499999 |      5690
    ##   -------
    ##   regions: 71 ranges and 0 metadata columns
    ##   seqinfo: 1 sequence from an unspecified genome; no seqlengths

    IS.hic.tab <- create.hic.table(hmec.IS, nhek.IS)

To shorten computational time, or if one is only interested in a subsection of a Hi-C matrix, one may wish to use a subset of the `hic.table` object. Use the `subset.dist` or `subset.index` options, see help for the `create.hic.table` function.

## Total Sum Scaling

If you are performing your `HiCcompare` analysis on the entire genome you can perform total sum scaling on the data before performing loess normalization. This requires the use of a list of `hic.table` objects, one for each chromosome. Additionally, when you create these `hic.table` objects you must set `scale = FALSE`. Once you have your list of `hic.table` objects you can then perform total sum scaling.

    hic.list <- total_sum(hic.list)

It is recommended to use total sum scaling when performing a `HiCcompare` analysis on the entire genome. If you are only using data for a single chromosome then total sum scaling should be equivalent to the `scale` option in the `create.hic.table` function.

## Joint Normalization

Now that you have created a `hic.table` object you can jointly normalize your two Hi-C matrices. The `hic_loess` function has many options and can accept a single `hic.table` or a list of hic.tables. If for example you wish to perform joint normalization for every chromosome on two cell lines while utilizing parallel computing you can create a list containing the hic.tables for each chromosome.

To change the degree of the polynomial for the loess joint normalization you can utilize the `degree` option, default is 1 (linear regression). A user-defined span, or the amount of data used to build the loess model, can also be set with the `span` option. However if `span = NA` (the default) the automatic smoothing parameter selection process will run and determine the optimal span for the data. The type of selection process can be changed using the `loess.criterion` option. Available settings are `gcv` (the default) for generalized cross-validation or `aicc` for Akaike information criterion. The loess automatic smoothing parameter selection uses a customized version of the `fANCOVA::loess.as` function. For more information on parameter selection please see the `fANCOVA` reference manual. It is recommended to use the default settings. If you have already run `hic_loess` on a dataset and know the span or would like to use a specific span then manually setting the span to a value can significantly reduce computation time especially for high resolution data.

`hic_loess` can utilize the `BiocParallel` package to perform parallel computing and lower computation time. The `parallel` option (FALSE by default) will only speed up computation if a list of hic.tables is entered into the function, i.e., it parallelizes processing of several chromosome-specific matrices. This is useful for performing joint normalization for every chromosome between two Hi-C datasets. For more information on `BiocParallel` see the reference manual here.

The basis of `HiCcompare` rests on the novel concept termed the MD plot. The MD plot is similar to the MA plot or the Bland-Altman plot. \(M\) is the log2 difference between the interaction frequencies from the two datasets. \(D\) is the unit distance between the two interacting regions. Loess is performed on the data after it is represented in the MD coordinate system. To visualize the MD plot the `Plot` option can be set to TRUE.

If you wish to detect differences between the two Hi-C datasets immediately following joint normalization you can set the `check.differences` option to TRUE. However, if you only want to jointly normalize the data for now keep this option set to FALSE. The difference detection process will be covered in the next section.

    # Jointly normalize data for a single chromosome
    hic.table <- hic_loess(chr22.table, Plot = TRUE, Plot.smooth = FALSE)

    ## Span for loess: 0.219052588777294

    ## GCV for loess: 0.000118686898199309

    ## AIC for loess: -0.212037314500057

    ## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
    ## ℹ Please use `linewidth` instead.
    ## ℹ The deprecated feature was likely used in the HiCcompare package.
    ##   Please report the issue at <https://github.com/dozmorovlab/HiCcompare/issues>.
    ## This warning is displayed once per session.
    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

    ## `geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

    ## `geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

    knitr::kable(head(hic.table))

chr1 | start1 | end1 | chr2 | start2 | end2 | IF1 | IF2 | D | M | adj.IF1 | adj.IF2 | adj.M | mc | A
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
chr22 | 16000000 | 16500000 | chr22 | 16000000 | 16500000 | 5 | 5.203323 | 0 | 0.0575053 | 5.103586 | 5.097713 | -0.0016611 | 0.0591664 | 5.100650
chr22 | 16000000 | 16500000 | chr22 | 16500000 | 17000000 | 2 | 8.672206 | 1 | 2.1163990 | 2.079392 | 8.341096 | 2.0040748 | 0.1123242 | 5.210244
chr22 | 16500000 | 17000000 | chr22 | 16500000 | 17000000 | 297 | 480.440193 | 0 | 0.6938939 | 303.153008 | 470.688840 | 0.6347275 | 0.0591664 | 386.920924
chr22 | 16000000 | 16500000 | chr22 | 17000000 | 17500000 | 5 | 14.742750 | 2 | 1.5600056 | 5.294664 | 13.922271 | 1.3947836 | 0.1652220 | 9.608468
chr22 | 16500000 | 17000000 | chr22 | 17000000 | 17500000 | 92 | 277.510581 | 1 | 1.5928370 | 95.652053 | 266.915059 | 1.4805129 | 0.1123242 | 181.283556
chr22 | 17000000 | 17500000 | chr22 | 17000000 | 17500000 | 5690 | 9435.359752 | 0 | 0.7296489 | 5807.880851 | 9243.853028 | 0.6704825 | 0.0591664 | 7525.866939

    # Multiple hic.tables can be processed in parallel by entering a list of hic.tables
    hic.list <- hic_loess(hic.list, parallel = TRUE)

The `hic_loess` joint normalization function extends the `hic.table` with the adjusted interaction frequencies, adjusted “M”, the “mc” correction factor, and the average expression “A”.

## Difference Detection

the MD plot is used to represent the differences \(M\) between two normalized datasets at a distance \(D\). Normalized \(M\) values are centered around 0 and the distribution at each distance remains fairly consistent. The \(M\) values are approximately normally distributed. \(M\) values are converted to Z-scores using the standard approach:

\[ Z_i = \frac{M_i - \bar{M}}{\sigma_M} \] where \(\bar{M}\) is the mean value of all \(M\)’s on the chromosome and \(\sigma_M\) is the standard deviation of all \(M\) values on the chromosome and \(i\) is the \(i\)th interacting pair on the chromosome.

During Z-score conversion the average expression of each interacting pair is considered. Due to the nature of \(M\), a difference represented by an interacting pair with IFs 1 and 10 is equivalent to an interacting pair of IFs 10 and 100 with both differences having an \(M\) value of 3.32. However the average expression of these two differences is 5.5 and 55, respectively. Differences with higher average expression are more trustworthy than those with low average expression due to the fact that a relatively small difference on the raw scale can lead to a large log2 fold change. Additionally since the IFs represent Hi-C sequencing reads, lower average numbers of reads are also less trustworthy. Thus we filter out differences with low average expression before calculating Z-scores when average expression (\(A\)) is less than a user set quantile (typically 5-20%) or a user set specific value of \(A\). The Z-scores can then be converted to p-values using the standard normal distribution.

To determine how to filter your data you can use the `filter_params()` function. This will produce a plot of the Matthews Correlation Coefficient (MCC) vs. the A minimum value filtered out. This plot should help you determine a reasonable value to set your filtering parameter in `hic_compare`. You may need to adjust the `numChanges` option and the `FC` option depending on the resolution of the data and how noisy it is.

Here we check the filtering:

    filter_params(hic.table)

Difference detection can be performed using the `hic_compare()` function. Before difference detection you will need to decide how you would like to filter out interactions with low average expression. You can filter based on a specific value of A. Once you have a normalized `hic.table` or list of `hic.tables` detect differences with an A filter as follows:

    hic.table <- hic_compare(hic.table, A.min = 15, adjust.dist = TRUE, p.method = 'fdr', Plot = TRUE)

    ## Filtering out interactions with A < 15

If you leave the `A.min = NA` then the 10th percentile of A will be calculated and used for filtering by default. The resulting table will display the results as shown below:

    knitr::kable(head(hic.table))

chr1 | start1 | end1 | chr2 | start2 | end2 | IF1 | IF2 | D | M | adj.IF1 | adj.IF2 | adj.M | mc | A | Z | p.value | p.adj
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
chr22 | 16000000 | 16500000 | chr22 | 16000000 | 16500000 | 5 | 5.203323 | 0 | 0.0575053 | 5.103586 | 5.097713 | -0.0016611 | 0.0591664 | 5.10065 | NA | 1.0000000 | 1.0000000
chr22 | 16500000 | 17000000 | chr22 | 16500000 | 17000000 | 297 | 480.440193 | 0 | 0.6938939 | 303.153008 | 470.688840 | 0.6347275 | 0.0591664 | 386.92092 | 1.2636692 | 0.2063488 | 0.8469872
chr22 | 17000000 | 17500000 | chr22 | 17000000 | 17500000 | 5690 | 9435.359752 | 0 | 0.7296489 | 5807.880851 | 9243.853028 | 0.6704825 | 0.0591664 | 7525.86694 | 1.3334594 | 0.1823811 | 0.8469872
chr22 | 17500000 | 18000000 | chr22 | 17500000 | 18000000 | 17641 | 23887.590475 | 0 | 0.4373290 | 18006.472072 | 23402.751072 | 0.3781626 | 0.0591664 | 20704.61157 | 0.7628794 | 0.4455353 | 0.8469872
chr22 | 18000000 | 18500000 | chr22 | 18000000 | 18500000 | 27241 | 22369.087265 | 0 | -0.2842733 | 27805.357163 | 21915.068475 | -0.3434397 | 0.0591664 | 24860.21282 | -0.6456180 | 0.5185268 | 0.8469872
chr22 | 18500000 | 19000000 | chr22 | 18500000 | 19000000 | 10592 | 8412.039485 | 0 | -0.3324475 | 10811.436550 | 8241.302792 | -0.3916139 | 0.0591664 | 9526.36967 | -0.7396494 | 0.4595127 | 0.8469872

Where `Z` is the Z-score calculated for the interaction (Z-scores with NA values result from filtering based on A), `p.value` is the un-adjusted p-value based on the standard normal distribution, and `p.adj` is the p-value after the multiple testing correction specified was applied.

## Converting `HiCcompare` results to `InteractionSet` objects

If after running `hic_loess` or `hic_compare` on your data you wish to perform additional analyses which require the `GRanges` object class you can convert the results using the `make_InteractionSet` function. This function will produce an `InteractionSet` object with the genomic ranges contained in the `hic.table` along with several metadata files containing the additional information produced by `hic_loess` or `hic_compare`.

    IntSet <- make_InteractionSet(hic.table)

## Simulating Hi-C Data

`HiCcompare` includes functions for simulating Hi-C data. The `hic_simulate` function allows you to simulate two Hi-C matrices with added bias and true differences at a specified fold change. As an example we will simulate two matrices with 250 true differences added at a fold change of 4.

    number_of_unitdistances <- 100 # The dimensions of the square matrix to be simualted
    number_of_changes       <- 250 # How many cells in the matrix will have changes
    i.range <- sample(1:number_of_unitdistances, number_of_changes, replace = TRUE) # Indexes of cells to have controlled changes
    j.range <- sample(1:number_of_unitdistances, number_of_changes, replace = TRUE) # Indexes of cells to have controlled changes

    sim_results <- hic_simulate(nrow = number_of_unitdistances, medianIF = 50000, sdIF = 14000, powerlaw.alpha = 1.8, fold.change = 4, i.range = i.range, j.range = j.range, Plot = TRUE, alpha = 0.1)

    ## Span for loess: 0.17494785405107

    ## GCV for loess: 0.000109174407533109

    ## AIC for loess: 0.339824119313794

    ## Filtering out interactions with A < 101

    ## True Positives: 191 Total added differences: 194 True Negatives: 4430

    ## TPR: 0.984536082474227

    ## SPC: 0.982261640798226

The results of the simulation are saved in a list.

    names(sim_results)

    ## [1] "TPR"       "SPC"       "pvals"     "hic.table" "true.diff" "truth"     "sim.table"

TPR is the true positive rate, SPC is the specificity, pvals is a vector of the p-values for every cell in the matrices, hic.table is the resulting hic.table object after `hic_loess` and `hic_compare` have been applied to the simulated data, true.diff is a table for the cells that had the specified fold change applied to them, truth is a vector of 0’s and 1’s indicating if a cell had a true difference applied - this is useful for input into ROC packages, sim.table is the simulated data in a hic.table object before being scaled, normalized, and analyzed for differences.

The `sim_matrix` function will produce two simulated Hi-C matrices without performing any analysis.

    sims <- sim_matrix(nrow = number_of_unitdistances, medianIF = 50000, sdIF = 14000, powerlaw.alpha = 1.8, fold.change = 4,
                       i.range = i.range, j.range = j.range)

## Additional Functions

`HiCcompare` contains some additional functions that may be useful.

If you do not choose to show the MD plots when you initially run `hic_loess` or `hic_compare` you can use the `MD.plot1` or `MD.plot2` functions. `MD.plot1` will create a side by side MD plot showing before and after loess normalization. Enter your original M and D vectors along with the M correction factor, `mc`, calculated by `hic_loess`. The `smooth` option controls if the plot is plotted using `smoothScatter` or as a `ggplot2` scatter plot.

    MD.plot1(M = hic.table$M, D = hic.table$D, mc = hic.table$mc, smooth = TRUE)

`MD.plot2` will create a standard MD plot with optional coloring based on p-value. Just enter an M and D vector and a p-value vector if desired.

    # no p-value coloring
    MD.plot2(M = hic.table$adj.M, D = hic.table$D, smooth = FALSE)

    # p-value coloring
    MD.plot2(M = hic.table$adj.M, D = hic.table$D, hic.table$p.value, smooth = FALSE)

There are two matrix transformation functions included. `sparse2full` will transform a sparse upper triangular matrix to a full Hi-C matrix. `full2sparse` will transform a full Hi-C matrix to sparse upper triangular format.

    full.NHEK <- sparse2full(NHEK.chr22)

    ## Matrix dimensions: 71x71

    full.NHEK[1:5, 1:5]

    ##          1.6e+07 16500000 1.7e+07 17500000 1.8e+07
    ## 1.6e+07        6       10      17       13       1
    ## 16500000      10      554     320      118      23
    ## 1.7e+07       17      320   10880     2922     576
    ## 17500000      13      118    2922    27545    3693
    ## 1.8e+07        1       23     576     3693   25794

    sparse.NHEK <- full2sparse(full.NHEK)
    head(sparse.NHEK)

    ##     region1  region2    IF
    ##       <num>    <num> <num>
    ## 1: 16000000 16000000     6
    ## 2: 16000000 16500000    10
    ## 3: 16500000 16500000   554
    ## 4: 16000000 17000000    17
    ## 5: 16500000 17000000   320
    ## 6: 17000000 17000000 10880

`KRnorm` will perform Knight-Ruiz normalization on a Hi-C matrix. Just enter the full Hi-C matrix to be normalized.

    KR.NHEK <- KRnorm(full.NHEK)

`SCN` will perform Sequential Component Normalization on a Hi-C matrix. Just enter the full Hi-C matrix to be normalized.

    SCN.NHEK <- SCN(full.NHEK)

`MA_norm` will perform MA normalization on a `hic.table` object.

    result <- MA_norm(hic.table, Plot = TRUE)

## Using HiCcompare on a cluster

Below is an example script for using `HiCcompare` on a computing cluster. The data was concatenated into a single sparse matrix for each group, containing information for all the chromosomes.

    library(HiCcompare)
    library(BiocParallel)

    args = commandArgs(trailingOnly=TRUE)

    dat1 <- read.table(args[1], header=FALSE, col.names=c("chr1", "start1", "end1", "chr2", "start2", "end2", "IF"))
    dat2 <- read.table(args[2], header=FALSE, col.names=c("chr1", "start1", "end1", "chr2", "start2", "end2", "IF"))

    dat1 <- dat1[dat1$chr1==dat1$chr2, ]
    dat2 <- dat2[dat2$chr1==dat2$chr2, ]

    dat1 <- split(dat1, dat1$chr1)
    dat2 <- split(dat2, dat2$chr1)

    hic.list <- mapply(create.hic.table, dat1, dat2, SIMPLIFY = FALSE, scale=FALSE)

    hic.list <- total_sum(hic.list)

    register(MulticoreParam(workers = 10), default = TRUE)

    hic.list <- hic_loess(hic.list, Plot=TRUE, parallel=TRUE)
    hic.list <- hic_compare(hic.list, A.min = NA, adjust.dist = TRUE, p.method = 'fdr', Plot = TRUE, parallel=TRUE)

    hic.list <- do.call(rbind, hic.list)

    hic.list <- hic.list[hic.list$p.adj<0.05,]

    write.table(hic.list, args[3])

The above can be saved as an R script and then submitted to a cluster using the following submission script.

    #!/bin/sh
    # Sun Grid Engine options (lines prefixed with #$)
    #$ -cwd
    #$ -N HiCCompare
    #$ -l h_rt=06:00:00
    #$ -l h_vmem=32G
    #$ -pe sharedmem 11
    #$ -V

    Rscript 01_HiCcompare.R $1 $2 $3

    qsub 01_launch_HiCcompare.sh dat1.1000000.pixels.tsv dat2.1000000.pixels.tsv hiccompare_1Mb.tsv

Credit to Ilya Flyamer (@Phlya on GitHub) for this example of using `HiCcompare` on a cluster.

# Session Info

    ## R version 4.6.0 (2026-04-24)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    ##
    ## time zone: Etc/UTC
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] HiCcompare_1.34.0 dplyr_1.2.1       rmarkdown_2.31
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] SummarizedExperiment_1.42.0 gtable_0.3.6                xfun_0.57                   bslib_0.10.0                ggplot2_4.0.3               rhdf5_2.54.1                Biobase_2.72.0              lattice_0.22-9              rhdf5filters_1.22.0         vctrs_0.7.3                 tools_4.6.0                 generics_0.1.4              stats4_4.6.0                parallel_4.6.0
    ## [15] tibble_3.3.1                pkgconfig_2.0.3             pheatmap_1.0.13             Matrix_1.7-5                KernSmooth_2.23-26          data.table_1.18.2.1         RColorBrewer_1.1-3          S7_0.2.2                    S4Vectors_0.50.0            lifecycle_1.0.5             compiler_4.6.0              farver_2.1.2                Seqinfo_1.2.0               codetools_0.2-20
    ## [29] InteractionSet_1.40.0       htmltools_0.5.9             sys_3.4.3                   buildtools_1.0.0            sass_0.4.10                 yaml_2.3.12                 pillar_1.11.1               jquerylib_0.1.4             BiocParallel_1.46.0         DelayedArray_0.38.0         cachem_1.1.0                abind_1.4-8                 nlme_3.1-169                gtools_3.9.5
    ## [43] tidyselect_1.2.1            digest_0.6.39               labeling_0.4.3              maketools_1.3.2             splines_4.6.0               fastmap_1.2.0               grid_4.6.0                  cli_3.6.6                   SparseArray_1.12.0          magrittr_2.0.5              S4Arrays_1.12.0             withr_3.0.2                 scales_1.4.0                XVector_0.52.0
    ## [57] matrixStats_1.5.0           gridExtra_2.3               evaluate_1.0.5              knitr_1.51                  GenomicRanges_1.64.0        IRanges_2.46.0              mgcv_1.9-4                  rlang_1.2.0                 Rcpp_1.1.1-1.1              glue_1.8.1                  BiocGenerics_0.58.0         jsonlite_2.0.0              R6_2.6.1                    Rhdf5lib_1.32.0
    ## [71] MatrixGenerics_1.24.0