Man pages for graumannlab/readat
Functionality to Read and Manipulate SomaLogic ADAT files
| aptamers | Sequence data for the Somalogic SOMAscan assay |
| as.ExpressionSet | Convert objects into ExpressionSets or MSnSets. |
| as.SummarizedExperiment | Convert objects into SummarizedExperiments |
| chromosomalPositions | Chromosomal Positions by SomaLogic AptamerId |
| colnamesStartWithSeqId | Does the input contain Sequence ID column names? |
| convertSeqIdToAptamer | Convert SeqIds to Aptamers |
| createSampleSubmission | Create a SomaLogic Sample Submission Form |
| ensemblIds | Ensembl IDs by SomaLogic AptamerId |
| extractSampleData | Extract the sample datasets |
| getChromosomalPositions | Get Chromosomal Positions by AptamerId |
| getEnsemblIds | Get Ensembl IDs by AptamerId |
| getGoMolecularFunctions | GO definitions by AptamerId |
| getKeggDefinitions | KEGG definitions, modules, and pathways by AptamerId |
| getPfam | Get PFAM IDs by AptamerId |
| getSampleIdVar | Get name of sample id variable |
| getSequencesWithLargestBetweenGroupVariation | Get sequences with the largest between group variation |
| getUniProtKeywords | Get UniProt Keywords by AptamerId |
| goMolecularFunction | GO definitions by SomaLogic AptamerId |
| isPass | Is the value a pass |
| isSomaEset | Is object a soma eset? |
| keggDefinitions | KEGG definitions, modules, and pathways by SomaLogic... |
| melt.WideSomaLogicData | Melt a WideSomaLogicData object |
| orderPlatePosition | Order Plate position |
| pfam | PFAM IDs by SomaLogic AptamerId |
| readAdat | Read a SomaLogic data file |
| readat-defunct | Defunct objects in readat |
| readComments | Read SomaLogic Sample Submission Comments File |
| readControls | Read SomaLogic Sample Submission Controls File |
| readFirstChar | Read the first character of each line |
| readSamples | Read SomaLogic Sample Submission Samples File |
| readSlides | Read SomaLogic Sample Submission Slides File |
| sub-.WideSomaLogicData | Indexing for WideSomaLogicData objects |
| uniprotKeywords | UniProt Keywords by SomaLogic AptamerId |
| WideSomaLogicData | Create a WideSomaLogicData object |
| WideSomaLogicDataAttributes | Get WideSomaLogicData attributes |
| writeSampleSubmissionForm | Write a SomaLogic sample submission form |
