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AllGenerics
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Placeholder for generics functions documentation |
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show(<AssayLink>) updateObject(<AssayLinks>) updateObject(<AssayLink>) AssayLink() AssayLinks() assayLink() assayLinks() `[`(<AssayLink>,<character>,<ANY>,<ANY>) `[`(<AssayLinks>,<list>,<ANY>,<ANY>) addAssayLink() addAssayLinkOneToOne()
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Links between Assays |
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aggregateFeatures(<QFeatures>) aggregateFeatures(<SummarizedExperiment>) adjacencyMatrix(<QFeatures>) `adjacencyMatrix<-`() aggcounts(<SummarizedExperiment>)
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Aggregate an assay's quantitative features |
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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()
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Quantitative MS QFeatures |
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VariableFilter() filterFeatures(<QFeatures>,<AnnotationFilter>) filterFeatures(<QFeatures>,<formula>)
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Filter features based on their rowData |
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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>)
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Managing missing data |
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logTransform(<SummarizedExperiment>) logTransform(<QFeatures>) scaleTransform(<SummarizedExperiment>) scaleTransform(<QFeatures>) normalize(<SummarizedExperiment>) normalize(<QFeatures>) sweep(<SummarizedExperiment>) sweep(<QFeatures>)
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QFeatures processing |
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subsetByFeature
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Subset by feature name |
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countUniqueFeatures()
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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. |
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display()
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Interactive MultiAssayExperiment Explorer |
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feat1
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Feature example data |
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feat3
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Example QFeatures object after processing |
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hlpsms
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hyperLOPIT PSM-level expression data |
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impute impute(<SummarizedExperiment>) impute(<QFeatures>)
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Quantitative proteomics data imputation |
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joinAssays()
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Join assays in a QFeatures object |
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readQFeatures() readSummarizedExperiment()
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QFeatures from tabular data |
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reduceDataFrame() expandDataFrame()
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Reduces and expands a DataFrame |
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unfoldDataFrame()
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Unfold a data frame |