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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# misha
<!-- badges: start -->
[![CRAN status](https://www.r-pkg.org/badges/version/misha)](https://CRAN.R-project.org/package=misha)
[![R-CMD-check](https://github.com/tanaylab/misha/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tanaylab/misha/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
The `misha` package is a toolkit for analysis of genomic data. it implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis.
## Installation
You can install the released version of misha from [CRAN](https://CRAN.R-project.org) with:
```{r, eval=FALSE}
install.packages("misha")
```
And the development version from GitHub with:
```{r, eval=FALSE}
remotes::install_github("tanaylab/misha")
```
## Usage
See the [Genomes](https://tanaylab.github.io/misha/articles/Genomes.html) vignette for instructions on how to create a misha database for common genomes.
See the [user manual](https://tanaylab.github.io/misha/articles/Manual.html) for more usage details.
#### Running scripts from old versions of misha (< 4.2.0)
Starting in `misha` 4.2.0, the package no longer stores global variables such as `ALLGENOME` or `GROOT`. Instead, these variables are stored in a special environment called `.misha`. This means that scripts written for older versions of `misha` will no longer work. To run such scripts, either add a prefix of `.misha$` to all those variables (`.misha$ALLGENOME` instead of `ALLGENOME`), or run the following command before running the script:
```{r, eval=FALSE}
ALLGENOME <<- .misha$ALLGENOME
GROOT <<- .misha$GROOT
ALLGENOME <<- .misha$ALLGENOME
GINTERVID <<- .misha$GINTERVID
GITERATOR.INTERVALS <<- .misha$GITERATOR.INTERVALS
GROOT <<- .misha$GROOT
GWD <<- .misha$GWD
GTRACKS <<- .misha$GTRACKS
```