---
title: "HiContactsData"
author: "Jacques Serizay"
date: "`r Sys.Date()`"
output: 
    BiocStyle::html_document
vignette: >
    %\VignetteIndexEntry{HiContactsData}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---

```{r, eval = TRUE, echo=FALSE, results="hide", message = FALSE, warning = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)
suppressPackageStartupMessages({
    library(HiContactsData)
})
```

## Introduction to HiContactsData 

HiContactsData is a companion data package giving programmatic access to 
several processed Hi-C files for demonstration, such as cool, mcool and 
pairs files. It is meant to be used with `HiContacts`. 

```{r}
library(HiContactsData)
```

The only function provided by HiContactsData package is `HiContactsData()`. 
Several files are available using this function, namely: 

- S288C fastq files (R1 & R2) (`sample`: `yeast_wt`, `format` = `fastq_R{12}`)
- S288C HiCool processing log (`sample`: `yeast_wt`, `format` = `HiCool_log`)
- S288C.cool (`sample`: `yeast_wt`, `format` = `cool`)
- S288C.mcool (`sample`: `yeast_wt`, `format` = `mcool`)
- S288C_G1.mcool (`sample`: `yeast_g1`, `format` = `mcool`)
- S288C_G2M.mcool (`sample`: `yeast_g1`, `format` = `mcool`)
- S288C_G1.pairs (`sample`: `yeast_g2m`, `format` = `pairs`)
- S288C_G2M.pairs (`sample`: `yeast_g2m`, `format` = `pairs`)
- S288C.hic (`sample`: `yeast_wt`, `format` = `hic`)
- S288C.hicpro.matrix (`sample`: `yeast_wt`, `format` = `hicpro_matrix`)
- S288C.hicpro.bed (`sample`: `yeast_wt`, `format` = `hicpro_bed`)
- S288C.pairs.gz for chrII only (`sample`: `yeast_wt`, `format` = `pairs`)
- S288C_Eco1-AID.mcool (`sample`: `yeast_Eco1`, `format` = `mcool`)
- S288C_Eco1-AID.pairs.gz for chrII only (`sample`: `yeast_Eco1`, `format` = `pairs`)
- mESCs.mcool (`sample`: `mESCs`, `format` = `mcool`)
- mESCs.pairs.gz for chr13 only (`sample`: `mESCs`, `format` = `pairs`)
- microC_HFFc6_chr17.mcool (`sample`: `microC`, `format` = `mcool`)

Yeast data comes from [Bastie, Chapard et al., Nature Structural & Molecular Biology 2022](https://doi.org/10.1038/s41594-022-00780-0) 
and mouse ESC data comes from [Bonev et al., Cell 2017](https://doi.org/10.1016/j.cell.2017.09.043). 
Human HcFF6 micro-C data comes from [Krietenstein et al., Mol. Cell 2020](https://doi.org/10.1016/j.molcel.2020.03.003).

To download one of these files, one can specify a `sample` and a file `format`:

```{r}
cool_file <- HiContactsData()
cool_file <- HiContactsData(sample = 'yeast_wt', format = 'cool')
cool_file
```

## HiContacts and HiContactsData

`HiCExperiment` package can be used to import data provided by `HiContactsData`. 
Refer to `HiCExperiment` package documentation for further information. 

## Session info

```{r}
sessionInfo()
```