---
title: "Description of chromhmmData"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{chromhmmData}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

To install `chromhmmData` use

```{r installation,eval=FALSE}
if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("chromhmmData")
```

```{r setup}
library(chromhmmData)
```

This package include the genomic annotations required for running `ChromHMM`.

This includes:

1. `CHROMSIZES`: text files with the chromosomes' sizes
2. `COORDS`: bed files with the coordinates of different genomic features
3. `ANCHORFILES`: text files with transcription start and end sites of known 
genes

The annotations for four different genomes are included in the package. Those
are the human `hg18` and `hg19` and the mouse `mm10` and `mm9`.

Use `system.file` to access the files and directorys. For example

```{r example}
# access a directory
chromsizes <- system.file('extdata/CHROMSIZES', package = 'chromhmmData')
dir(chromsizes)

# access a file
system.file('extdata/CHROMSIZES', 'hg19.txt', package = 'chromhmmData')
```

These annotation files are obtained from 
[`ChromHMM`](https://github.com/jernst98/ChromHMM) source code repository.


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