Package index

QFeatures class

The QFeatures class

QFeatures() show(<QFeatures>) plot(<QFeatures>) `[`(<QFeatures>,<ANY>,<ANY>,<ANY>) `[`(<QFeatures>,<character>,<ANY>,<ANY>) c(<QFeatures>) dims(<QFeatures>) nrows(<QFeatures>) ncols(<QFeatures>) rowData(<QFeatures>) `rowData<-`(<QFeatures>,<DataFrameList>) `rowData<-`(<QFeatures>,<ANY>) rbindRowData() selectRowData() rowDataNames() `names<-`(<QFeatures>,<character>) addAssay() removeAssay() replaceAssay() `[[<-`(<QFeatures>,<ANY>,<ANY>) updateObject(<QFeatures>) dropEmptyAssays()

Quantitative MS QFeatures

longForm(<QFeatures>) longForm(<SummarizedExperiment>)

Reshape into a long data format

joinAssays()

Join assays in a QFeatures object

show(<AssayLink>) updateObject(<AssayLinks>) updateObject(<AssayLink>) AssayLink() AssayLinks() assayLink() assayLinks() `[`(<AssayLink>,<character>,<ANY>,<ANY>) `[`(<AssayLinks>,<list>,<ANY>,<ANY>) addAssayLink() addAssayLinkOneToOne()

Links between Assays

countUniqueFeatures()

Count Unique Features

createPrecursorId()

Create precursor identfiers

display()

Interactive MultiAssayExperiment Explorer

Data import

Create QFeatures and SummarizedExperiment object

readSummarizedExperiment() readQFeatures()

QFeatures from tabular data

readQFeaturesFromDIANN()

Read DIA-NN output as a QFeatures objects

Missing data

Filtering and handling of missing values

zeroIsNA(<SummarizedExperiment>,<missing>) zeroIsNA(<QFeatures>,<integer>) zeroIsNA(<QFeatures>,<numeric>) zeroIsNA(<QFeatures>,<character>) infIsNA(<SummarizedExperiment>,<missing>) infIsNA(<QFeatures>,<integer>) infIsNA(<QFeatures>,<numeric>) infIsNA(<QFeatures>,<character>) nNA(<SummarizedExperiment>,<missing>) nNA(<QFeatures>,<integer>) nNA(<QFeatures>,<numeric>) nNA(<QFeatures>,<character>) filterNA(<SummarizedExperiment>) filterNA(<QFeatures>)

Managing missing data

impute impute(<SummarizedExperiment>) impute(<QFeatures>)

Quantitative proteomics data imputation

QFeatures processing

Quantitative data processing

logTransform(<SummarizedExperiment>) logTransform(<QFeatures>) scaleTransform(<SummarizedExperiment>) scaleTransform(<QFeatures>) normalize(<SummarizedExperiment>) normalize(<QFeatures>) sweep(<SummarizedExperiment>) sweep(<QFeatures>)

QFeatures processing

Feature aggregations

Feature aggregations

aggregateFeatures(<QFeatures>) aggregateFeatures(<SummarizedExperiment>) adjacencyMatrix(<QFeatures>) `adjacencyMatrix<-`() aggcounts(<SummarizedExperiment>)

Aggregate assays' quantitative features

Filtering

Feature filtering

VariableFilter() filterFeatures(<QFeatures>,<AnnotationFilter>) filterFeatures(<QFeatures>,<formula>) isDuplicated()

Filter features based on their rowData

subsetByFeature subsetByFeature,QFeatures,character-method

Subset by feature name

Example data

Example data

feat1

Feature example data

feat3

Example QFeatures object after processing

feat4

Example QFeatures

hlpsms

hyperLOPIT PSM-level expression data

DataFrame

DataFrame functions

reduceDataFrame() expandDataFrame()

Reduces and expands a DataFrame

unfoldDataFrame()

Unfold a data frame

Generic functions

Package generics

AllGenerics

Placeholder for generics functions documentation