paristools.Rmd

---
title: "Introduction to paristools"
author: "Zhuoer Dong"
date: "`r Sys.Date()`"
output: prettydoc::html_pretty
vignette: >
  %\VignetteIndexEntry{Introduction to paristools}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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



```{r message=FALSE}
library(paristools)
library(ggplot2)
```



# read files

```{r}
sam_file <- system.file('extdata', 'Neat1_1.Aligend_trunc.sam', package = 'paristools')

mapping <- read_sam(sam_file)
mapping
```

```{r}
duplexgroup_file <- system.file('extdata', 'Neat1_1.duplexgroup', package = 'paristools');

duplex_group <- read_duplexgroup(duplexgroup_file)
duplex_group
```

refer to `read_bed()`



# calculate coverage

## reference coverage

```{r}
loc_df <- mapping |> sam_to_loc_df() 
loc_df

ref_coverage <- loc_df |> cal_coverage()
ref_coverage
```

```{r}
ggplot(ref_coverage) + 
    geom_col(aes(pos, n_reads)) + 
    facet_wrap(~strand, ncol = 1) + 
    labs(x = 'position', y = 'number of reads')
```

## duplex group segment average coverage 

```{r}
dg_coverage <- get_dg_coverage(duplex_group, ref_coverage)
dg_coverage
```

```{r}
dg_coverage |> dplyr::select(-strand) |> tidyr::spread('pair', 'n_reads') |>
    ggplot() + geom_point(aes(left, right))
```



# others 

```{r}
mapping |> dplyr::mutate(strand = purrr::map_chr(FLAG, paristools:::get_strand))
```