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Quick Start

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):
wget -O win-x64.zip https://github.com/Genometric/MSPC/releases/latest/download/win-x64.zip
  1. Extract the downloaded archive and browse to the containing directory:
unzip win-x64.zip -d mspc; cd mspc

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

  1. Download sample data:
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:

.\mspc.exe -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:

.
โ””โ”€โ”€ session_20191126_222131330
โ”œโ”€โ”€ ConsensusPeaks.bed
โ”œโ”€โ”€ ConsensusPeaks_mspc_peaks.txt
โ”œโ”€โ”€ EventsLog_20191126_2221313409928.txt
โ”œโ”€โ”€ rep1
โ”‚ย ย  โ”œโ”€โ”€ Background.bed
โ”‚ย ย  โ”œโ”€โ”€ Background_mspc_peaks.txt
โ”‚ย ย  โ”œโ”€โ”€ Confirmed.bed
โ”‚ย ย  โ”œโ”€โ”€ Confirmed_mspc_peaks.txt
โ”‚ย ย  โ”œโ”€โ”€ Discarded.bed
โ”‚ย ย  โ”œโ”€โ”€ Discarded_mspc_peaks.txt
โ”‚ย ย  โ”œโ”€โ”€ FalsePositive.bed
โ”‚ย ย  โ”œโ”€โ”€ FalsePositive_mspc_peaks.txt
โ”‚ย ย  โ”œโ”€โ”€ Stringent.bed
โ”‚ย ย  โ”œโ”€โ”€ Stringent_mspc_peaks.txt
โ”‚ย ย  โ”œโ”€โ”€ TruePositive.bed
โ”‚ย ย  โ”œโ”€โ”€ TruePositive_mspc_peaks.txt
โ”‚ย ย  โ””โ”€โ”€ Weak.bed
โ”‚ย ย  โ”œโ”€โ”€ Weak_mspc_peaks.txt
โ””โ”€โ”€ rep2
ย ย  โ”œโ”€โ”€ Background.bed
ย ย  โ”œโ”€โ”€ Background_mspc_peaks.txt
ย ย  โ”œโ”€โ”€ Confirmed.bed
ย ย  โ”œโ”€โ”€ Confirmed_mspc_peaks.txt
ย ย  โ”œโ”€โ”€ Discarded.bed
ย ย  โ”œโ”€โ”€ Discarded_mspc_peaks.txt
ย ย  โ”œโ”€โ”€ FalsePositive.bed
ย ย  โ”œโ”€โ”€ FalsePositive_mspc_peaks.txt
ย ย  โ”œโ”€โ”€ Stringent.bed
ย  โ”œโ”€โ”€ Stringent_mspc_peaks.txt
ย ย  โ”œโ”€โ”€ TruePositive.bed
ย ย  โ”œโ”€โ”€ TruePositive_mspc_peaks.txt
ย ย  โ””โ”€โ”€ Weak.bed
โ””โ”€โ”€ 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#