Package: PerseusR 0.3.4

Jan Rudolph

PerseusR: 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>.

Authors:Jan Rudolph <[email protected]>

PerseusR_0.3.4.tar.gz
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PerseusR_0.3.4.tgz(r-4.4-any)PerseusR_0.3.4.tgz(r-4.3-any)
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PerseusR.pdf |PerseusR.html✨
PerseusR/json (API)
NEWS

# Install 'PerseusR' in R:
install.packages('PerseusR', repos = c('https://cox-labs.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/cox-labs/perseusr/issues

On CRAN:

bioinformaticsinteropmaxquantperseusproteomics

5.82 score 12 stars 55 scripts 242 downloads 1 mentions 29 exports 14 dependencies

Last updated 2 years agofrom:d15bcf4009. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winNOTENov 12 2024
R-4.5-linuxNOTENov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:annotColsannotCols<-annotRowsannotRows<-as.ExpressionSet.matrixDataas.matrixData.ExpressionSetboolParamValuedescriptiondescription<-imputeDataimputeData<-intParamValuemainmain<-matrixDataMatrixDataCheckmultiChoiceParamValueparseParametersqualityDataqualityData<-read.perseusread.perseus.as.ExpressionSetread.perseus.as.listread.perseus.as.matrixDataread.perseus.defaultsingleChoiceParamIndsingleChoiceParamValuestringParamValuewrite.perseus

Dependencies:BiobaseBiocGenericscligenericsgluelifecyclemagrittrplyrRcpprlangstringistringrvctrsXML

Using Perseus data in R

PerseusR Team

Rendered fromUsing-Perseus-data-in-R.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2018-10-24
Started: 2018-09-21

Readme and manuals

Help Manual

Help pageTopics
Get annotation columnsannotCols
Set annotation columnsannotCols<-
Get annotation rowsannotRows
Set annotation rowsannotRows<-
Coerces a MatrixData into an ExpressionSetas.ExpressionSet.matrixData
Coerces an ExpressionSet into a MatrixDataas.matrixData.ExpressionSet
Bool parameter valueboolParamValue
Create annotation rowscreate_annotRows
Get column descriptiondescription
Set column descriptiondescription<-
Get imputation of main data frameimputeData
Set imputation of main data frameimputeData<-
Infer Perseus type annotation row from DataFrame column classesinfer_perseus_annotation_types
matrixData initializerinitialize,matrixData-method
Int parameter valueintParamValue
Get main columnsmain
Set main columnsmain<-
matrixData constructormatrixData
MatrixDatamatrixData-class
MatrixDataCheck: a function to check the validity of an object as a perseus data frameMatrixDataCheck MatrixDataCheck.default MatrixDataCheck.ExpressionSet MatrixDataCheck.list MatrixDataCheck.matrixData
Multiple choice valuemultiChoiceParamValue
Get namesnames,matrixData-method
Column names of main and annotation columnsnames.matrixData
Parse parametersparseParameters
Get quality values of main data framequalityData
Set quality values of main data framequalityData<-
Read Perseus matrix filesread.perseus read.perseus.as.ExpressionSet read.perseus.as.list read.perseus.as.matrixData read.perseus.default
Single choice indexsingleChoiceParamInd
Single choice valuesingleChoiceParamValue
String parameter valuestringParamValue
write.perseus: function to generate a perseus-readable text documentwrite.perseus write.perseus.data.frame write.perseus.default write.perseus.ExpressionSet write.perseus.list write.perseus.matrix write.perseus.matrixData