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| addAssay | Quantitative MS QFeatures |
| addAssayLink | Links between Assays |
| addAssayLinkOneToOne | Links between Assays |
| aggcounts | Aggregate an assay's quantitative features |
| aggcounts,SummarizedExperiment | Aggregate an assay's quantitative features |
| aggcounts-method | Aggregate an assay's quantitative features |
| aggregateFeatures | Aggregate an assay's quantitative features |
| aggregateFeatures-method | Aggregate an assay's quantitative features |
| AllGenerics | Placeholder for generics functions documentation |
| AssayLink | Links between Assays |
| assayLink | Links between Assays |
| AssayLink-class | Links between Assays |
| AssayLinks | Links between Assays |
| assayLinks | Links between Assays |
| AssayLinks-class | Links between Assays |
| CharacterVariableFilter | Filter features based on their rowData |
| CharacterVariableFilter-class | Filter features based on their rowData |
| class:AssayLink | Links between Assays |
| class:AssayLinks | Links between Assays |
| class:QFeatures | Quantitative MS QFeatures |
| 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. |
| dims-method | Quantitative MS QFeatures |
| display | Interactive MultiAssayExperiment Explorer |
| expandDataFrame | Reduces and expands a 'DataFrame' |
| feat1 | Feature example data |
| feat2 | Feature example data |
| feat3 | Example 'QFeatures' object after processing |
| filterFeatures | Filter features based on their rowData |
| filterFeatures-method | Filter features based on their rowData |
| filterNA | Managing missing data |
| filterNA-method | Managing missing data |
| ft_na | Feature example data |
| hlpsms | hyperLOPIT PSM-level expression data |
| impute | Quantitative proteomics data imputation |
| impute-method | Quantitative proteomics data imputation |
| infIsNA | Managing missing data |
| infIsNA-method | Managing missing data |
| joinAssays | Join assays in a QFeatures object |
| logTransform | QFeatures processing |
| logTransform-method | QFeatures processing |
| longFormat | Quantitative MS QFeatures |
| missing-data | Managing missing data |
| names<--method | Quantitative MS QFeatures |
| nNA | Managing missing data |
| nNA-method | Managing missing data |
| normalize | QFeatures processing |
| normalize-method | QFeatures processing |
| normalizeMethods | QFeatures processing |
| NumericVariableFilter | Filter features based on their rowData |
| NumericVariableFilter-class | Filter features based on their rowData |
| plot.QFeatures | Quantitative MS QFeatures |
| QFeatures | Quantitative MS QFeatures |
| QFeatures-class | Quantitative MS QFeatures |
| QFeatures-filtering | Filter features based on their rowData |
| QFeatures-processing | QFeatures processing |
| rbindRowData | Quantitative MS QFeatures |
| readQFeatures | QFeatures from tabular data |
| readSummarizedExperiment | QFeatures from tabular data |
| reduceDataFrame | Reduces and expands a 'DataFrame' |
| rowData-method | Quantitative MS QFeatures |
| rowData<--method | Quantitative MS QFeatures |
| rowDataNames | Quantitative MS QFeatures |
| scaleTransform | QFeatures processing |
| scaleTransform-method | QFeatures processing |
| selectRowData | Quantitative MS QFeatures |
| se_na2 | Feature example data |
| show-method | Links between Assays |
| show-method | Quantitative MS QFeatures |
| subsetByFeature | Subset by feature name |
| subsetByFeature-method | Subset by feature name |
| sweep | QFeatures processing |
| sweep-method | QFeatures processing |
| VariableFilter | Filter features based on their rowData |
| zeroIsNA | Managing missing data |
| zeroIsNA-method | Managing missing data |
| [-method | Links between Assays |
| [-method | Quantitative MS QFeatures |