---
title: "Genome arithmetics"
author: "Aditya M Bhagwat"
date: "`r Sys.Date()`"
output: BiocStyle::html_document
vignette: >
  %\VignetteIndexEntry{genome_arithmetics}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include=TRUE, echo=FALSE, message=FALSE}
knitr::opts_chunk$set(echo = TRUE, collapse = TRUE, cache = FALSE)
#str(knitr::opts_chunk$get())
```

<!-- ![](../inst/extdata/readme.png) -->

# Introduction {-}

This vignette discusses multicrispr's genome arithmetics functionality, often required in the first step of Crispr/Cas9 design.
Multicrispr's genome arithmetics functions allow two-way transformations around a genomic range's start/end. The `r Biocpkg("GenomicRanges")` and `r Biocpkg("plyranges")` packages also offer an extensive genome arithmetics functionality, though with functions designed as one-way transformations.

We illustrate the different operations on a small GRanges with four prime editing targets in Anazlone et al. (2019)

```{r, fig.width=5.5, fig.height=3, out.width="85%"}
require(multicrispr)
bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38  
gr <- char_to_granges(c(PRNP  = 'chr20:4699600:+',         # snp
                        HBB  = 'chr11:5227002:-',            # snp
                        HEXA = 'chr15:72346580-72346583:-',  # del
                        CFTR = 'chr7:117559593-117559595:+'),# ins
                     bsgenome = bsgenome)
plot_intervals(gr, facet_var = c('targetname','seqnames'))
```

# Genome arithmetics {-}

## Extend {-}

```{r, fig.width=5.5, fig.height=3, out.width="85%"}
ext <- extend(gr, start = -10, end = +10, plot = TRUE)
```

## Up flank {-}

```{r, fig.width=5.5, fig.height=3, out.width="85%"}
up <- up_flank(gr,  -22,  -1, plot=TRUE, facet_var=c('targetname', 'seqnames'))
```

## Down flank {-}

```{r, fig.width=5.5, fig.height=3, out.width="85%"}
dn <- down_flank(gr, +1, +22, plot=TRUE)
```

## Double flank {-}

```{r, fig.width=5.5, fig.height=3, out.width="85%"}
dbl <- double_flank(gr, -10,  -1, +1, +20, plot = TRUE)
```

# References {-}

Anzalone, A.V., Randolph, P.B., Davis, J.R. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019). https://doi.org/10.1038/s41586-019-1711-4