Pathifier is an algorithm designed to model the heterogeneity of a set of samples by calculating their level of deregulation based on their genomic data in a pathway based manner.
The following scripts may be used for easier loading of data, and the calculation of default arguments not implemented in the native functions. As well as fast customized plotting of the results of the deregulation analysis.
An R script for running Pathifier (Drier et al., 2013) in R.
First file required is TAB separated file of the gene expression matrix in the following format:
| NAME | Sample1 | Sample2 | Sample3 | Sample n... |
|---|---|---|---|---|
| NORMALS | 1 | 1 | 0 | ... |
| Gene1 | 1.25 | 1.56 | 2.56 | ... |
| Gene2 | 4.56 | 0.25 | 1.75 | ... |
| Gene3 | 1.56 | 3.21 | 1.36 | ... |
| GeneN | ... | ... | ... | ... |
1st row = Sample names 2nd row = Normal status of samples: 1 = Healthy, 0 = Tumor 1st col = Gene names from third row on (Gene symbol format is recommended)
Second file required by the script is a TAB separated file of the pathway information in GMT format:
| PATHWAY1 | Blank cell | GeneA | GeneB | GeneC | etc... |
| PATHWAY2 | Blank cell | GeneD | GeneA | GeneX | etc... |
Notes:
- NO HEADER ROW!
- Gene names used must coincide between expression matrix and pathway annotation
- GMT format: Each row represents a pathway. 1st column is pathway name or id, 2nd column it's discarded BUT needed, from the 3rd column on starts the genes belonging to that pathway.
Test-data is provided on TEST-DATA directory
Powered by package(s): "pathifier"
An R script for showing results of Pathifier (Drier et al., 2013) in a heatmap, showing the deregulation of each sample by pathway.
This script works directly with the results of the "1_Run_Pathifier.R" script and the stand-alone version of Pathifier, adding a vector for depicting normal samples (See additional notes).
The last update of the heatmap adds sample labeling for normal (healthy) vs tumoral samples
Output preview (using EXAMPLE_DATA)
Powered by package(s): "gplots", "RColorBrewer"
An R script with 2 functions for plotting the principal curves derived of the pathway deregulation analysis using Pathifier (Drier et al., 2013)
This script works directly with the results of "1_Run_Pathifier.R" script and the stand-alone version of Pathifier, adding a vector for depicting normal samples (See additional notes).
Output examples (using EXAMPLE_DATA)
Powered by package(s): "plotly", "RColorBrewer"
Pathifier Stand-alone version: http://www.weizmann.ac.il/complex/compphys/software/yotam/pathifier/installation.html
R-version of Pathifier is available via Bioconductor: http://bioconductor.org/packages/pathifier/