PerseusR

Convenience functions for interop between Perseus and R.

Designed to work with the PluginInterop plugin for the Perseus framework.

Citation

If you use PerseusR in your projects, please cite

Rudolph, J D and Cox, J 2018, A network module for the Perseus software for computational proteomics facilitates proteome interaction graph analysis doi:10.1101/447268

Installation

Make sure to have R >= 3.5.0 installed. Paste the following lines into an running R session. You can skip the comment lines starting with #.

# installing BioConductor dependencies first
install.packages('BiocManager')
BiocManager::install('Biobase')

# installing PerseusR
install.packages('PerseusR')

Usage

PerseusR provides two functions for reading and writing files from/to Perseus. You can use them to write simple scripts which can be used as MatrixProcessing activities in Perseus. Additionally you can parse Perseus parameters and extract their values.

an example R script that could be called though the Perseus plugin:

# if applicable: read command-line arguments
args = commandArgs(trailingOnly=TRUE)
if (length(args) != 3) {
    stop("Should provide three arguments: parameters inFile outFile", call.=FALSE)
}
paramFile <- args[1]
inFile <- args[2]
outFile <- args[3]

library(PerseusR)
# extract parameters
parameters <- parseParameters(paramFile)
networkType <- singleChoiceParamValue(parameters, "Network type")
corFnc <- singleChoiceParamValue(parameters, "Correlation function")
power <- intParamValue(parameters, "Power")
# read data
mdata <- read.perseus(inFile)

# if additional matrices are included, the additional information like imputation can be extracted.
imputeMatrix <- imputeData(mdata)
qualityMatrix <- qualityData(mdata)

# run any kind of analysis
library(WGCNA)
net <- blockwiseModules(t(main(mdata)), power = power, corFnc = corFnc, networkType = networkType)
c1 <- net$dendrograms[[1]]
df <- as.data.frame(cbind(c1$merge, c1$height))
colnames(df) <- c('left', 'right', 'distance')

# save results to matrixData and write to file
outMdata <- matrixData(main=df)
write.perseus(outMdata, outFile)

# save results to matrixData and write to file with additional matrices

outdata <- matrixData(main = combine, imputeData = imputeMatrix, qualityData = qualityMatrix)
write.perseus(outMdata, outFile)

Licensing and contributions

PerseusR is licensed under the MIT license. Contributions are welcome.