readCool: Read a .(m)cool file and return Hi-C data as a dataframe
In PhanstielLab/BentoBox: Coordinate-Based Genomic Visualization Package for R

readCool

R Documentation

Read a .(m)cool file and return Hi-C data as a dataframe

Description

Read a .(m)cool file and return Hi-C data as a dataframe

Usage

readCool(
    file,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    altchrom = NULL,
    altchromstart = NULL,
    altchromend = NULL,
    resolution = "auto",
    zrange = NULL,
    norm = "NONE",
    binChunkSize = 5e6,
    params = NULL,
    quiet = FALSE
)

Arguments

`file`	A character value specifying the path to the .(m)cool 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.
`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.
`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 .(m)cool file. Default value is `norm = "NONE"`.
`binChunkSize`	A numeric specifying the number of bin indices to read from a file for a given region at a given resolution. If the total amount of data is larger than the `binChunkSize`, data will be read in multiple chunks. Default value is `binChunkSize = 5e6`.
`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.

Author(s)

Sarah Parker, Nicole Kramer

Examples


## .cool file
coolFile <- file.path(tempdir(), "Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool")
download.file(url = "https://usgs2.osn.mghpcc.org/cooler01/examples/hg19/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool",
    destfile = coolFile)

## Read in region `chr2:10000000-22000000` at 1000Kb cool file resolution
coolData <- readCool(file = coolFile, chrom = "chr2", chromstart = 10000000,
                     chromend = 22000000,
                     resolution = 1000000)

## .mcool file
mcoolFile <- file.path(tempdir(), "LEUK_HEK_PJA27_inter_30.mcool")
download.file(url = "https://zenodo.org/records/10906240/files/LEUK_HEK_PJA27_inter_30.mcool?download=1",
    destfile = mcoolFile)

## Read in region `chr2:1000000-5000000` at 100Kb resolution
mcoolData_100Kb <- readCool(file = mcoolFile, chrom = "2",
                            chromstart = 1000000, chromend = 5000000,
                            resolution = 100000)

## Read in data for chr2 at 2500Kb resolution 
mcoolData_2500Kb <- readCool(file = mcoolFile, chrom = "2",
                             resolution = 2500000)

PhanstielLab/BentoBox documentation built on Feb. 27, 2025, midnight