Input/Output 'SomaScan' Data
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Documentation for package ‘SomaDataIO’ version 6.1.0
Help Pages
| $.soma_adat | The 'soma_adat' Class and S3 Methods |
| $<-.soma_adat | The 'soma_adat' Class and S3 Methods |
| ==.soma_adat | Group Generics for 'soma_adat' Class Objects |
| adat-helpers | Helpers to Extract Information from an ADAT |
| adat2eSet | Convert ADAT to ExpressionSet Object |
| addAttributes | Add Attributes to 'soma_adat' Objects |
| addClass | Add a Class to an Object |
| add_rowid | Helpers for Working With Row Names |
| annotations | Analyte Annotations, Col.Meta, and Row Info |
| antilog | Group Generics for 'soma_adat' Class Objects |
| apt2seqid | Working with SomaLogic SeqIds |
| checkSomaScanVersion | Helpers to Extract Information from an ADAT |
| cleanNames | Clean Up Character String |
| Col.Meta | Analyte Annotations, Col.Meta, and Row Info |
| col2rn | Helpers for Working With Row Names |
| collapseAdats | Load ADAT files as a list |
| colmeta | Analyte Annotations, Col.Meta, and Row Info |
| diffAdats | Diff Two ADAT Objects |
| example_data | Example Data and Objects |
| ex_analytes | Example Data and Objects |
| ex_anno_tbl | Example Data and Objects |
| ex_target_names | Example Data and Objects |
| getAdatVersion | Helpers to Extract Information from an ADAT |
| getAnalyteInfo | Get Analyte Annotation Information |
| getAnalytes | Get Analytes |
| getFeatureData | Get Analyte Annotation Information |
| getFeatures | Get Analytes |
| getMeta | Get Analytes |
| getSeqId | Working with SomaLogic SeqIds |
| getSeqIdMatches | Working with SomaLogic SeqIds |
| getSignalSpace | Helpers to Extract Information from an ADAT |
| getSomamerData | Deprecated function(s) of the 'SomaDataIO' package |
| getSomamers | Deprecated function(s) of the 'SomaDataIO' package |
| getSomaScanLiftCCC | Helpers to Extract Information from an ADAT |
| getSomaScanVersion | Helpers to Extract Information from an ADAT |
| getTargetNames | Get Analyte Annotation Information |
| groupGenerics | Group Generics for 'soma_adat' Class Objects |
| has_rn | Helpers for Working With Row Names |
| is.apt | Working with SomaLogic SeqIds |
| is.intact.attributes | Are Attributes Intact? |
| is.SeqId | Working with SomaLogic SeqIds |
| is.soma_adat | Read (Load) SomaLogic ADATs |
| is_intact_attr | Are Attributes Intact? |
| is_lifted | Lift an ADAT Between Assay Versions |
| is_seqFormat | Test 'AptName' Format |
| lift_adat | Lift an ADAT Between Assay Versions |
| loadAdatsAsList | Load ADAT files as a list |
| locateSeqId | Working with SomaLogic SeqIds |
| matchSeqIds | Working with SomaLogic SeqIds |
| Math.soma_adat | Group Generics for 'soma_adat' Class Objects |
| median.soma_adat | The 'soma_adat' Class and S3 Methods |
| meltExpressionSet | Convert to Long Format |
| merge_clin | Merge Clinical Data into SomaScan |
| Ops.soma_adat | Group Generics for 'soma_adat' Class Objects |
| params | Common Parameters in 'SomaDataIO' |
| parseHeader | SomaLogic ADAT parser |
| pivotExpressionSet | Convert to Long Format |
| print.soma_adat | The 'soma_adat' Class and S3 Methods |
| read.adat | Read (Load) SomaLogic ADATs |
| read_adat | Read (Load) SomaLogic ADATs |
| read_annotations | Import a SomaLogic Annotations File |
| regexSeqId | Working with SomaLogic SeqIds |
| rm_rn | Helpers for Working With Row Names |
| rn2col | Helpers for Working With Row Names |
| rowmeta | Analyte Annotations, Col.Meta, and Row Info |
| rownames | Helpers for Working With Row Names |
| SeqId | Working with SomaLogic SeqIds |
| seqid2apt | Working with SomaLogic SeqIds |
| set_rn | Helpers for Working With Row Names |
| SomaDataIO-deprecated | Deprecated function(s) of the 'SomaDataIO' package |
| SomaScanObjects | Example Data and Objects |
| soma_adat | The 'soma_adat' Class and S3 Methods |
| Summary.soma_adat | Group Generics for 'soma_adat' Class Objects |
| summary.soma_adat | The 'soma_adat' Class and S3 Methods |
| transform | Scale Transform 'soma_adat' Columns/Rows |
| transform.soma_adat | Scale Transform 'soma_adat' Columns/Rows |
| write_adat | Write an ADAT to File |
| [.soma_adat | The 'soma_adat' Class and S3 Methods |
| [<-.soma_adat | The 'soma_adat' Class and S3 Methods |
| [[.soma_adat | The 'soma_adat' Class and S3 Methods |
| [[<-.soma_adat | The 'soma_adat' Class and S3 Methods |