All functions

AllGenerics

Placeholder for generics functions documentation

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

Links between Assays

aggregateFeatures(<QFeatures>) aggregateFeatures(<SummarizedExperiment>) aggcounts(<SummarizedExperiment>)

Aggregate an assay's quantitative features

show(<QFeatures>) plot(<QFeatures>) `[`(<QFeatures>,<ANY>,<ANY>,<ANY>) dims(<QFeatures>) `[`(<QFeatures>,<character>,<ANY>,<ANY>) rowData(<QFeatures>) `rowData<-`(<QFeatures>,<DataFrameList>) `rowData<-`(<QFeatures>,<ANY>) rbindRowData() selectRowData() rowDataNames() `names<-`(<QFeatures>,<character>) longFormat() addAssay() updateObject(<QFeatures>) QFeatures()

Quantitative MS QFeatures

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

Filter features based on their rowData

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

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

QFeatures processing

subsetByFeature

Subset by feature name

countUniqueFeatures()

Count Unique Features This function counts the number of unique features per sample. A grouping structure can be provided to count higher level features from assays, for example counting the number of unique proteins from PSM data.

display()

Interactive MultiAssayExperiment Explorer

feat1

Feature example data

feat3

Example QFeatures object after processing

hlpsms

hyperLOPIT PSM-level expression data

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

Quantitative proteomics data imputation

joinAssays()

Join assays in a QFeatures object

readQFeatures() readSummarizedExperiment()

QFeatures from tabular data

reduceDataFrame() expandDataFrame()

Reduces and expands a DataFrame