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

In PhanstielLab/plotgardener: Coordinate-Based Genomic Visualization Package for R

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)                     

PhanstielLab/plotgardener documentation built on July 1, 2024, 7:06 p.m.