Skip to content

quick_start.md

Latest commit

 

History

History
260 lines (207 loc) · 6.2 KB

quick_start.md

File metadata and controls

260 lines (207 loc) · 6.2 KB
title Quick Start

import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem';

You may run MSPC as a command-line application, a C# library, or an R package available from Bioconductor. In the following, we provide quick start for using MSPC as a command-line application and an R package, and provide details in their respective pages.

Quick Start: Command-line

Preparation

  1. Install a self-contained release of MSPC, using either of following commands depending on your runtime (see installation page for detailed installation options):

<Tabs groupId="operating-systems" defaultValue="win" values={[ { label: 'Windows', value: 'win', }, { label: 'Linux', value: 'linux', }, { label: 'macOS', value: 'mac', }, ] }> 

wget -O win-x64.zip https://github.com/Genometric/MSPC/releases/latest/download/win-x64.zip
wget -O linux-x64.zip https://github.com/Genometric/MSPC/releases/latest/download/linux-x64.zip
wget -O osx-x64.zip https://github.com/Genometric/MSPC/releases/latest/download/osx-x64.zip
  1. Extract the downloaded archive and browse to the containing directory:

<Tabs groupId="operating-systems" defaultValue="win" values={[ { label: 'Windows', value: 'win', }, { label: 'Linux', value: 'linux', }, { label: 'macOS', value: 'mac', }, ] }> 

unzip win-x64.zip -d mspc; cd mspc
unzip -q linux-x64.zip -d mspc && cd mspc && chmod +x mspc
unzip -q osx-x64.zip -d mspc && cd mspc && chmod +x mspc

Notice that if you are working on Windows x64, you will need to download the program unzip.

  1. Download sample data:

<Tabs groupId="operating-systems" defaultValue="win" values={[ { label: 'Windows', value: 'win', }, { label: 'Linux', value: 'linux', }, { label: 'macOS', value: 'mac', }, ] }> 

wget -O demo.zip https://github.com/Genometric/Annotations/raw/master/SampleFiles/demo.zip; unzip demo.zip -d .
wget -O demo.zip https://github.com/Genometric/Annotations/raw/master/SampleFiles/demo.zip && unzip demo.zip -d .
wget -O demo.zip https://github.com/Genometric/Annotations/raw/master/SampleFiles/demo.zip && unzip demo.zip -d .

Run

To run MSPC use the following command depending on your runtime:

<Tabs groupId="operating-systems" defaultValue="win" values={[ { label: 'Windows', value: 'win', }, { label: 'Linux', value: 'linux', }, { label: 'macOS', value: 'mac', }, ] }> 

.\mspc.exe -i .\rep*.bed -r bio -w 1e-4 -s 1e-8
./mspc -i rep*.bed -r bio -w 1e-4 -s 1e-8
./mspc -i rep*.bed -r bio -w 1e-4 -s 1e-8

Output

MSPC creates a folder in the current execution path named session_X_Y, where X and Y are execution date and time respectively, which contains the following files and folders:

.
└── session_20191126_222131330
    ├── ConsensusPeaks.bed
	├── ConsensusPeaks_mspc_peaks.txt
	├── EventsLog_20191126_2221313409928.txt
    ├── rep1
    │   ├── Background.bed
    │   ├── Background_mspc_peaks.txt
    │   ├── Confirmed.bed
    │   ├── Confirmed_mspc_peaks.txt
    │   ├── Discarded.bed
    │   ├── Discarded_mspc_peaks.txt
    │   ├── FalsePositive.bed
    │   ├── FalsePositive_mspc_peaks.txt
    │   ├── Stringent.bed
    │   ├── Stringent_mspc_peaks.txt
    │   ├── TruePositive.bed
    │   ├── TruePositive_mspc_peaks.txt
    │   └── Weak.bed
    │   ├── Weak_mspc_peaks.txt
    └── rep2
        ├── Background.bed
        ├── Background_mspc_peaks.txt
        ├── Confirmed.bed
        ├── Confirmed_mspc_peaks.txt
        ├── Discarded.bed
        ├── Discarded_mspc_peaks.txt
        ├── FalsePositive.bed
        ├── FalsePositive_mspc_peaks.txt
        ├── Stringent.bed
        ├── Stringent_mspc_peaks.txt
        ├── TruePositive.bed
        ├── TruePositive_mspc_peaks.txt
        └── Weak.bed
        └── Weak_mspc_peaks.txt

:::info Note that in these instructions you download a self-contained deployment of MSPC, hence you do not need to install .NET (or any other dependencies) for the program to execute.

For other installation options see the installation page.
:::

Quick Start: R package

MSPC is also distributed as a Bioconductor package. To use in R programming language, you may take the following steps.

Install and Load

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("rmspc")

library(rmspc)

Run

# Load example data available in the package.
path <- system.file("extdata", package = "rmspc")

# Run MSPC
results <- mspc(
        input = input, 
        replicateType = "Technical",
        stringencyThreshold = 1e-8,
        weakThreshold = 1e-4, 
        gamma = 1e-8,
        keep = FALSE,
        GRanges = TRUE,
        multipleIntersections = "Lowest",
        c = 2,
        alpha = 0.05)

:::info The MSPC R package can load data from files and Granges objects. For a complete documentation on the package, please refer to the bioconductor documentation. :::

See Also