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Mirstat

A Simple tool to analyze QPCR data from miRNA

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MirStat

Simple tool to analyze miRNA QPCR data

Motivation

MirStat is an R script developed to analyze miRNA data obtained by QPCR arrays. It generates a principal component analyze for the first 3 dimensions and a heatmap for each predefined groups. Developed for the study: Teichenne et al, Transcriptional profile of acinar cells reprogrammed into insulin producing cells, 2015

Principle

MirStat.R is a simple R script which analyzes QPCR values from a CSV file (see example in /data). Users can modify the existing groups in the first part of the code so it can match their own sample names.

For each group: For each qPCR, 1 sample with an NA or all samples with undetermined values will trigger its exclusion from the group analysis. The remaining qPCR data are reduced, centered and classified by hierarchical cluster analysis. A principal component analyze is performed with FactoMineR package and summarized by graphs and tables in both individual and variable spaces. Finally, a distance matrix is generated by the Pearson method and subsequently used to create a heatmap scaled by individual sample thanks to gplots package.

Get MirStat

From github repository

git clone https://github.com/a-slide/MirStat
sudo chmod u+x MirStat.R

You may also add the executable to your system PATH

Usage

First, the R script code had to be edited with your own sample name to create as many group as needed. Just add a new vector line as shown below

# Create a list of group names to analyze data separately
v1 = c("sample1-1", "sample1-2", "sample1-3", "sample2-1", "sample2-2", "sample2-3")
v2 = c("sample2-1", "sample2-2", "sample2-3", "sample3-1", "sample3-2", "sample3-3")

Update the group list and group name vector to match your group names

# Define group list and group names
group.list = list(v1,v2)
names(group.list) = c("sample1 vs sample2", "sample2 vs sample3")

Format your tab separated csv data sheet as follow:

            qPCR1   qPCR2   qPCR3   ...
sample1-1   0.23    0       12334   ...
sample1-2   12      0       8755    ...
sample1-3   65      0       87545   ...
...         ...     ...     ...     ...

See example file in the data folder

Run the script with the data sheet path as only argument

Usage: MirStat.R my ./path/myQPCRresult.csv

All file will be generated in the current folder

Dependencies:

The program was developed under Linux Mint 16 "petra" but is compatible with other LINUX debian based distributions. Not tested under windows or Mac

Program

Third party R packages

Authors and Contact

Adrien Leger - 2015