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| $-method | Accessing and modifying information in MultiAssayExperiment |
| $<--method | Accessing and modifying information in MultiAssayExperiment |
| anyReplicated | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| anyReplicated-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| assay-method | ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE) |
| assay-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| assays-method | ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE) |
| assays-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| c-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| coerce-ExperimentList | ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE) |
| coerce-method | ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE) |
| coerce-method | MatchedAssayExperiment - A matched-samples MultiAssayExperiment class |
| coerce-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| coerce-MultiAssayExperiment | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| colData-method | Accessing and modifying information in MultiAssayExperiment |
| colData<--method | Accessing and modifying information in MultiAssayExperiment |
| colnames<--method | Accessing and modifying information in MultiAssayExperiment |
| complete.cases-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| DataFrame | Objects exported from other packages |
| dimnames-method | ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE) |
| dimnames-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| ExperimentList | Represent multiple experiments as a List-derivative 'ExperimentList' |
| ExperimentList-class | ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE) |
| experiments | Accessing and modifying information in MultiAssayExperiment |
| experiments-method | Accessing and modifying information in MultiAssayExperiment |
| experiments<- | Accessing and modifying information in MultiAssayExperiment |
| experiments<--method | Accessing and modifying information in MultiAssayExperiment |
| exportClass | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| exportClass-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| getWithColData | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| hasAssay | Checking assay method for any class |
| hasRowRanges | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| hasRowRanges-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| HDF5MultiAssayExperiment | Save a MultiAssayExperiment class object to HDF5 and Rds files |
| intersectColumns | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| intersectRows | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| isEmpty-method | ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE) |
| isEmpty-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| length-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| listToMap | Convert map from data.frame or DataFrame to list and vice versa |
| loadHDF5MultiAssayExperiment | Save a MultiAssayExperiment class object to HDF5 and Rds files |
| longFormat | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| makeHitList | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| makeMatchList | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| mapToList | Convert map from data.frame or DataFrame to list and vice versa |
| MatchedAssayExperiment | MatchedAssayExperiment - A matched-samples MultiAssayExperiment class |
| MatchedAssayExperiment-class | MatchedAssayExperiment - A matched-samples MultiAssayExperiment class |
| mergeReplicates | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| mergeReplicates-method | ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE) |
| mergeReplicates-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| metadata-method | Accessing and modifying information in MultiAssayExperiment |
| metadata<--method | Accessing and modifying information in MultiAssayExperiment |
| miniACC | Adrenocortical Carcinoma (ACC) MultiAssayExperiment |
| MultiAssayExperiment | Construct an integrative representation of multi-omic data with 'MultiAssayExperiment' |
| MultiAssayExperiment-class | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| MultiAssayExperiment-helpers | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| MultiAssayExperiment-methods | Accessing and modifying information in MultiAssayExperiment |
| MultiAssayExperimentToMAF | Convert MultiAssayExperiment to MAF class |
| names-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| names<--method | Accessing and modifying information in MultiAssayExperiment |
| prepMultiAssay | Prepare a 'MultiAssayExperiment' instance |
| reexports | Objects exported from other packages |
| renameColname | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| renamePrimary | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| replicated | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| replicated-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| sampleMap | Accessing and modifying information in MultiAssayExperiment |
| sampleMap-method | Accessing and modifying information in MultiAssayExperiment |
| sampleMap<- | Accessing and modifying information in MultiAssayExperiment |
| sampleMap<--method | Accessing and modifying information in MultiAssayExperiment |
| saveHDF5MultiAssayExperiment | Save a MultiAssayExperiment class object to HDF5 and Rds files |
| show-method | ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE) |
| show-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| splitAssays | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| splitAssays-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| subset | Subsetting a MultiAssayExperiment object |
| subsetBy | Subsetting a MultiAssayExperiment object |
| subsetByAssay | Subsetting a MultiAssayExperiment object |
| subsetByAssay-method | Subsetting a MultiAssayExperiment object |
| subsetByColData | Subsetting a MultiAssayExperiment object |
| subsetByColData-method | Subsetting a MultiAssayExperiment object |
| subsetByColumn | Subsetting a MultiAssayExperiment object |
| subsetByColumn-method | Subsetting a MultiAssayExperiment object |
| subsetByRow | Subsetting a MultiAssayExperiment object |
| subsetByRow-method | Subsetting a MultiAssayExperiment object |
| updateObject-method | MultiAssayExperiment - An integrative multi-assay class for experiment data |
| upsetSamples | Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in 'UpSetR' |
| wideFormat | A group of helper functions for manipulating and cleaning a MultiAssayExperiment |
| [-method | Subsetting a MultiAssayExperiment object |
| [<--method | Subsetting a MultiAssayExperiment object |
| [[-method | Subsetting a MultiAssayExperiment object |
| [[<--method | Subsetting a MultiAssayExperiment object |