VHSE-scales (principal components score Vectors of Hydrophobic, Steric, and Electronic properties), is derived from principal components analysis (PCA) on independent families of 18 hydrophobic properties, 17 steric properties, and 15 electronic properties, respectively, which are included in total 50 physicochemical variables of 20 coded amino acids.

Click here to download VHSE-Scales code.

Click here to download example input data.

Before using VHSE-Scales, make sure that you have the R language and the R packages Peptides, doParallel, entropy, dplyr, readxl, stringr installed on your computer. If not, after installing R, run the following commands to install the dependencies in R respectively.

`install.packages("doParallel")`
`install.packages("Peptides")`
`install.packages("dplyr")`
`install.packages("stringr")`
`install.packages("readxl")`
`install.packages("entropy")`

Creat a working directory, e.g., ./working
Unzip the downloaded file in the working directory
Run VHSE-Scales:
path-to-Rscript vhse_calculate.R -i <Input file(csv)> -o <Working directory>


Parameters:

-i: A csv file with two columns. The first column is the sequence of neoantigen's WT Peptide, while the second column is the sequence of neoantigen's Mutant Peptide. Now only neoantigens with nine peptides and one site-specific mutation are supported for calculation. You can download the example data by clicking on the link above.
-o: Working directory. The folder's path which you put the unziped files in, and where the output files will be located.


Example:

/usr/bin/Rscript vhse_calculate.R -i example.csv -o /feature_calculate/