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

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>)

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

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