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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

# installing 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]

# 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
net <- blockwiseModules(t(main(mdata)), power = power, corFnc = corFnc, networkType = networkType)
c1 <- net$dendrograms[[1]]
df <-$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.

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PerseusR documentation built on May 2, 2019, 6:52 a.m.