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Convenience functions for interop between Perseus and R.
Designed to work with the PluginInterop plugin for the Perseus framework.
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
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')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)PerseusR is licensed under the MIT license.
Contributions are welcome.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.