Package: QFeatures 1.17.0

Laurent Gatto

QFeatures: Quantitative features for mass spectrometry data

The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

Authors:Laurent Gatto [aut, cre], Christophe Vanderaa [aut]

QFeatures_1.17.0.tar.gz
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QFeatures.pdf |QFeatures.html✨
QFeatures/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/rformassspectrometry/qfeatures/issues

Datasets:
  • feat1 - Feature example data
  • feat2 - Feature example data
  • feat3 - Example 'QFeatures' object after processing
  • ft_na - Feature example data
  • hlpsms - HyperLOPIT PSM-level expression data
  • se_na2 - Feature example data

On BioConductor:QFeatures-1.17.0(bioc 3.21)QFeatures-1.16.0(bioc 3.20)

infrastructuremassspectrometryproteomicsmetabolomicsbioconductormass-spectrometry

11.45 score 25 stars 48 packages 251 scripts 3.5k downloads 47 exports 98 dependencies

Last updated 2 months agofrom:4049f6fea0. Checks:OK: 1 ERROR: 5 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winERRORDec 19 2024
R-4.5-linuxERRORDec 19 2024
R-4.4-winERRORDec 19 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winERRORDec 19 2024
R-4.3-macERRORDec 19 2024

Exports:addAssayaddAssayLinkaddAssayLinkOneToOneadjacencyMatrixadjacencyMatrix<-aggcountsaggregateFeaturesassayLinkAssayLinkassayLinksAssayLinkscoercecountUniqueFeaturesdimsdisplaydropEmptyAssaysexpandDataFramefilterFeaturesfilterNAimputeinfIsNAjoinAssayslogTransformlongFormatncolsnNAnormalizenrowsQFeaturesrbindRowDatareadQFeaturesreadQFeaturesFromDIANNreadSummarizedExperimentreduceDataFrameremoveAssayreplaceAssayrowData<-rowDataNamesscaleTransformselectRowDatashowsubsetByFeaturesweepunfoldDataFrameupdateObjectVariableFilterzeroIsNA

Dependencies:abindAnnotationFilteraskpassbase64encBiobaseBiocBaseUtilsBiocGenericsbslibcachemcliclueclustercolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMultiAssayExperimentmunsellnlmeopensslpillarpkgconfigplotlyplyrpromisesProtGenericspurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorssassscalesSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc

Data visualization from a QFeatures object

Laurent Gatto

Rendered fromVisualization.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-04-04
Started: 2021-07-19

Processing quantitative proteomics data with QFeatures

Laurent Gatto

Rendered fromProcessing.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-04-04
Started: 2019-12-14

Quantitative features for mass spectrometry data

Laurent Gatto

Rendered fromQFeatures.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-04-05
Started: 2020-07-14

Readme and manuals

Help Manual

Help pageTopics
Aggregate an assay's quantitative featuresadjacencyMatrix,QFeatures-method adjacencyMatrix,SummarizedExperiment-method adjacencyMatrix<- aggcounts aggcounts,SummarizedExperiment-method aggregateFeatures aggregateFeatures,QFeatures-method aggregateFeatures,SummarizedExperiment-method
Placeholder for generics functions documentationAllGenerics
Links between AssaysaddAssayLink addAssayLinkOneToOne AssayLink assayLink AssayLink-class AssayLinks assayLinks AssayLinks-class class:AssayLink class:AssayLinks show,AssayLink-method updateObject,AssayLink-method updateObject,AssayLinks-method [,AssayLink,character,ANY,ANY-method [,AssayLink,character-method [,AssayLinks,character-method [,AssayLinks,list,ANY,ANY-method
Count Unique FeaturescountUniqueFeatures
Interactive MultiAssayExperiment Explorerdisplay
Feature example datafeat1 feat2 ft_na se_na2
Example 'QFeatures' object after processingfeat3
hyperLOPIT PSM-level expression datahlpsms
Quantitative proteomics data imputationimpute impute,QFeatures-method impute,SummarizedExperiment-method
Join assays in a QFeatures objectjoinAssays
Managing missing datafilterNA filterNA,QFeatures-method filterNA,SummarizedExperiment-method infIsNA infIsNA,QFeatures,character-method infIsNA,QFeatures,integer-method infIsNA,QFeatures,missing-method infIsNA,QFeatures,numeric-method infIsNA,SummarizedExperiment,missing-method missing-data nNA nNA,QFeatures,character-method nNA,QFeatures,integer-method nNA,QFeatures,missing-method nNA,QFeatures,numeric-method nNA,SummarizedExperiment,missing-method zeroIsNA zeroIsNA,QFeatures,character-method zeroIsNA,QFeatures,integer-method zeroIsNA,QFeatures,missing-method zeroIsNA,QFeatures,numeric-method zeroIsNA,SummarizedExperiment,missing-method
Quantitative MS QFeaturesaddAssay c,QFeatures-method class:QFeatures coerce,MultiAssayExperiment,QFeatures-method coerce-QFeatures dims,QFeatures-method dropEmptyAssays longFormat names<-,QFeatures,character-method ncols,QFeatures-method nrows,QFeatures-method plot.QFeatures QFeatures QFeatures-class rbindRowData removeAssay replaceAssay rowData,QFeatures-method rowData<-,QFeatures,ANY-method rowData<-,QFeatures,DataFrameList-method rowDataNames selectRowData show,QFeatures-method updateObject,QFeatures-method [,QFeatures,ANY,ANY,ANY-method [,QFeatures,character,ANY,ANY-method [[<-,QFeatures,ANY,ANY-method
Filter features based on their rowDataCharacterVariableFilter CharacterVariableFilter-class filterFeatures filterFeatures,QFeatures,AnnotationFilter-method filterFeatures,QFeatures,formula-method NumericVariableFilter NumericVariableFilter-class QFeatures-filtering VariableFilter
QFeatures processinglogTransform logTransform,QFeatures-method logTransform,SummarizedExperiment-method normalize normalize,QFeatures-method normalize,SummarizedExperiment-method normalizeMethods QFeatures-processing scaleTransform scaleTransform,QFeatures-method scaleTransform,SummarizedExperiment-method sweep sweep,QFeatures-method sweep,SummarizedExperiment-method
QFeatures from tabular datareadQFeatures readQFeatures,data.frame,data.frame readQFeatures,data.frame,vector readQFeatures,missing,vector readSummarizedExperiment
Read DIA-NN output as a QFeatures objectsreadQFeaturesFromDIANN
Reduces and expands a 'DataFrame'expandDataFrame reduceDataFrame
Subset by feature namesubsetByFeature subsetByFeature,QFeatures,character-method
Unfold a data frameunfoldDataFrame