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Description

Perseus R Interop.

Enables the interoperability between the Perseus platform for omics data analysis (Tyanova et al. 2016) <doi:10.1038/nmeth.3901> and R. It provides the foundation for developing and running Perseus plugins implemented in R by providing all required input and output handling, including data and parameter parsing as described in Rudolph and Cox 2018 <doi:10.1101/447268>.

PerseusR

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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 analysisdoi: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.

Metadata

Version

0.3.4

License

Unknown

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