readHic {plotgardener} | R Documentation

## Read a .hic file and return Hi-C data as a dataframe

### Description

Read a .hic file and return Hi-C data as a dataframe

### Usage

    readHic(
        file,
        chrom,
        chromstart = NULL,
        chromend = NULL,
        altchrom = NULL,
        altchromstart = NULL,
        altchromend = NULL,
        assembly = "hg38",
        resolution = "auto",
        res_scale = "BP",
        zrange = NULL,
        norm = "KR",
        matrix = "observed",
        params = NULL,
        quiet = FALSE
    )

### Arguments

`file` | A character value specifying the path to the .hic file.
`chrom` | Chromosome of data, as a string.
`chromstart` | Integer start position on chromosome.
`chromend` | Integer end position on chromosome.
`altchrom` | Alternate chromosome for interchromosomal data, as a string.
`altchromstart` | Alternate chromosome integer start position for interchromosomal data.
`altchromend` | Alternate chromosome integer end position for interchromosomal data.
`assembly` | Default genome assembly as a string or a assembly object. Default value is `assembly = "hg38"`.
`resolution` | A numeric specifying the width of each pixel. "auto" will attempt to choose a resolution in basepairs based on the size of the region.
`res_scale` | A character value specifying the resolution scale. Default value is `res_scale = "BP"`. Options are: `"BP"`: Base pairs. `"FRAG"`: Fragments.
`zrange` | A numeric vector of length 2 specifying the range of interaction scores, where extreme values will be set to the max or min.
`norm` | Character value specifying hic data normalization method. This value must be found in the .hic file. Default value is `norm = "KR"`.
`matrix` | Character value indicating the type of matrix to output. Default value is `matrix = "observed"`. Options are: `"observed"`: Observed counts. `"oe"`: Observed/expected counts. `"log2oe"`: Log2 transformed observed/expected counts.
`params` | An optional pgParams object containing relevant function parameters.
`quiet` | A logical indicating whether or not to print messages.

### Value

Returns a 3-column dataframe in sparse upper triangular format with the following columns: `chrom`, `altchrom`, `counts`.

### See Also

straw

### Examples

    hicFile <- system.file("extdata/test_chr22.hic", package="plotgardenerData")

    ## Read in data for all chr22 file at 2.5Mb bp resolution
    hicData <- readHic(file = hicFile, chrom = "22",
                        assembly = "hg19",
                        resolution = 2500000)

    ## Read in region `chr22:20000000-47500000` at 100 Kb resolution
    hicData10Kb <- readHic(file = hicFile, chrom = "22",
                            chromstart = 20000000, chromend = 47500000,
                            assembly = "hg19",
                            resolution = 100000)

[Package plotgardener version 1.0.17 Index]