# BerrySTR

**Repository Path**: matthew123/BerrySTR

## Basic Information

- **Project Name**: BerrySTR
- **Description**: 用于STR的图片生成
- **Primary Language**: R
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2016-06-02
- **Last Updated**: 2020-12-19

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# BerrySTR  -   Generate STR graphs

STR analysis is a molecular biology method used to compare specific loci on DNA from two or more samples. 
This program is based on R pacakge("Fragman") to generate the graphs which are used to detect chromosome abnormalities.

# The Steps to build R packages

## Build tar file for current version of package

Build the package like this:

```
R CMD build [project path, like './']
```

Then a tar.gz file will be created. You could check the package for error.

```
R CMD check *.tar.gz
```

Notice that all warnings and notes should be fixed before you release next version.
And then you could `INSTALL` the package:
```
R CMD INSTALL --no-multiarch --byte-compile *.tar.gz
```

Or use this for short

```
R CMD INSTALL --no-multiarch --build --preclean --byte-compile .
```

## RStudio: The Powerful IDE for R

**Rstudio** will do the previous steps automatically for you.

# App Usage

A builtin `app` function will parse the command line arguments, and call `pipeline_str_pic` by
its options. Return value could be used as a `quit` status.

The options list here:

| long | short | description |
| ---- | :---: | ----------- |
| --input.dir  | -i | Dir which stores all files. The path is absolute path |
| --output.dir | -o | Dir which stores all result pictures |
| --sample.list| -l | A file which show Correspondence between sample file and sample name |