scHiC

The scHiC package is designed for processing single-cell Hi-C data from raw FASTQ files to Hi-C contact matrices. This document provides detailed instructions on how to install and use this package, as well as a comprehensive API reference.

Installation

To install the scHiC package, you will need to have R and Bioconductor installed. Use the following commands in R to install the package:

# Install devtools if not already installed
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

# Install scHiC from GitHub
devtools::install_github("jlchen5/scHiC")

# Ensure you have also installed the necessary dependencies:

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

BiocManager::install(c("GenomicRanges", "Biostrings", "Rsamtools", "BiocParallel"))

Quick Start

To get started with the scHiC package, load it and read some sample FASTQ data:

library(scHiC)

# Paths to your FASTQ files
fastq_paths <- c("path/to/your/sample1.fastq", "path/to/your/sample2.fastq")

# Read and preprocess FASTQ data
data <- read_fastq_data_parallel(fastq_paths)

# Perform quality control
qc_data <- quality_control(data)

# Align reads using Bowtie2 (make sure Bowtie2 is installed and configured)
align_reads(fastq_paths, "path/to/output.sam", "path/to/bowtie2/index")

# Build contact matrix
contact_matrix <- build_contact_matrix("path/to/output.sam")

Functions read_fastq_data_parallel This function reads and preprocesses FASTQ files in parallel.

Arguments:

fastq_paths: A character vector of paths to FASTQ files. Returns:

A list of lists, each containing sequences and qualities extracted from one FASTQ file. Example:

fastq_paths <- c("sample1.fastq", "sample2.fastq")
data <- read_fastq_data_parallel(fastq_paths)

quality_control Performs quality control on sequence data.

Arguments:

data: A list containing sequences and qualities.
min_quality: The minimum mean quality score required (default: 20).
min_length: The minimum sequence length required (default: 50). Returns:

A list of the same structure as input but containing only the sequences and qualities that passed the quality control. Example:

qc_data <- quality_control(data)

align_reads Aligns reads to a reference genome using an external tool such as Bowtie2.

Arguments:

fastq_paths: A character vector of paths to FASTQ files.
output_path: Path where the output SAM file will be saved.
aligner_cmd: Command template to use for alignment, e.g., "bowtie2 -x %s -U %s -S %s".
aligner_options: Additional options for the aligner (default: "").
Returns:

None. Output is written directly to the file specified by output_path. Example:

align_reads(fastq_paths, "output.sam", "path/to/bowtie2/index")

build_contact_matrix Builds a Hi-C contact matrix from aligned read data.

Arguments:

bam_path: Path to the BAM file containing aligned read data. resolution: Resolution of the contact matrix (default: 1e6). Returns:

A contact matrix as a Matrix object. Example:

contact_matrix <- build_contact_matrix("output.sam")

Contributing

Contributions to the scHiC package are welcome. Please refer to the repository's issues and pull requests sections on GitHub to contribute or report problems.

License

This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.