---
title: "Importing Data"
author: "Shian Su"
output: html_document
vignette: >
  %\VignetteIndexEntry{Importing Data}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

# preload to avoid loading messages
library(NanoMethViz)
```

```{r}
library(NanoMethViz)
```

In order to use this package, your data must be converted from the output of
methylation calling software to a special tabix format. Due to the use of the
Unix `sort` function, this can only currently be done on a Linux or MacOS
system.

We currently support output from

* Nanopolish
* f5c

The conversion can be done using the `create_tabix_file()` function. We provide
example data of nanopolish output within the package, we can look inside to see
how the data looks coming out of nanopolish

```{r}
methy_calls <- system.file(package = "NanoMethViz",
    c("sample1_nanopolish.tsv.gz", "sample2_nanopolish.tsv.gz"))

# have a look at the first 10 rows of methy_data
methy_calls_example <- read.table(
    methy_calls[1], sep = "\t", header = TRUE, nrows = 6)

methy_calls_example
```

We then create a temporary path to store a converted file, this will be deleted
once you exit your R session. Once `create_tabix_file()` is run, it will create
a tabix file along with its index. Because we have a small amount of data, we
can read in a small portion of it to see how it looks, do not do this with large
datasets as it decompresses all the data and will take very long to run.

```{r, message=F}
methy_tabix <- file.path(tempdir(), "methy_data.bgz")
samples <- c("sample1", "sample2")

# you should see messages when running this yourself
create_tabix_file(methy_calls, methy_tabix, samples)

# don't do this with actual data
# we have to use gzfile to tell R that we have a gzip compressed file
methy_data <- read.table(
    gzfile(methy_tabix), col.names = methy_col_names(), nrows = 6)

methy_data
```

Now `methy_tabix` will be the path to a tabix object that is ready for use with
NanoMethViz. Please head over to the "Introduction" vignette to see how to use
this data for visualisation!
