bb_readHic.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/bb_readHic.R
\name{bb_readHic}
\alias{bb_readHic}
\title{Read a .hic file and return Hi-C data as a dataframe}
\usage{
bb_readHic(hicFile, chrom)
}
\arguments{
\item{hicFile}{A character value specifying the path to the .hic file.}

\item{chrom}{Chromosome of data, as a string.}

\item{chromstart}{Integer start position on chromosome.}

\item{chromend}{Integer end position on chromosome.}

\item{altchrom}{Alternate chromosome for interchromosomal data, as a string.}

\item{altchromstart}{Alternate chromosome integer start position for interchromosomal data.}

\item{altchromend}{Alternate chromosome integer end position for interchromosomal data.}

\item{assembly}{Default genome assembly as a string or a \link[BentoBox]{bb_assembly} object. Default value is \code{assembly = "hg19"}.}

\item{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.}

\item{res_scale}{A character value specifying the resolution scale. Default value is \code{res_scale = "BP"}. Options are:
\itemize{
\item{\code{"BP"}: }{Base pairs.}
\item{\code{"FRAG"}: }{Fragments.}
}}

\item{zrange}{A numeric vector of length 2 specifying the range of interaction scores, where extreme values will be set to the max or min.}

\item{norm}{Character value specifying hic data normalization method. This value must be found in the .hic file. Default value is \code{norm = "KR"}.}

\item{matrix}{Character value indicating the type of matrix to output. Default value is \code{matrix = "observed"}. Options are:
\itemize{
\item{\code{"observed"}: }{Observed counts.}
\item{\code{"oe"}: }{Observed/expected counts.}
}}

\item{params}{An optional \link[BentoBox]{bb_assembly} object containing relevant function parameters.}
}
\value{
Returns a 3-column dataframe in sparse upper triangular format with the following columns: \code{chrom}, \code{altchrom}, \code{counts}.
}
\description{
Read a .hic file and return Hi-C data as a dataframe
}
\seealso{
\link[strawr]{straw}
}