# Functionality to Read and Manipulate SomaLogic ADAT files

## Documentation for package ‘readat’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

aptamers | Sequence data for the Somalogic SOMAscan assay
as.ExpressionSet | Convert objects into ExpressionSets or MSnSets.
as.ExpressionSet.WideSomaLogicData | Convert objects into ExpressionSets or MSnSets.
as.matrix.WideSomaLogicData | Get WideSomaLogicData attributes
as.MSnSet | Convert objects into ExpressionSets or MSnSets.
as.MSnSet.WideSomaLogicData | Convert objects into ExpressionSets or MSnSets.
as.SummarizedExperiment | Convert objects into SummarizedExperiments
as.SummarizedExperiment.WideSomaLogicData | 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
defunct | Defunct objects in readat
ensemblIds | Ensembl IDs by SomaLogic AptamerId
extractSampleData | Extract the sample datasets
getChecksum | Get WideSomaLogicData attributes
getChromosomalPositions | Get Chromosomal Positions by AptamerId
getEnsemblIds | Get Ensembl IDs by AptamerId
getGoBiologicalProcesses | GO definitions by AptamerId
getGoCellularComponents | GO definitions by AptamerId
getGoMolecularFunctions | GO definitions by AptamerId
getIntensities | Get WideSomaLogicData attributes
getIntensities.LongSomaLogicData | Get WideSomaLogicData attributes
getIntensities.WideSomaLogicData | Get WideSomaLogicData attributes
getKeggDefinitions | KEGG definitions, modules, and pathways by AptamerId
getKeggModules | KEGG definitions, modules, and pathways by AptamerId
getKeggPathways | KEGG definitions, modules, and pathways by AptamerId
getMetadata | Get WideSomaLogicData attributes
getPfam | Get PFAM IDs by AptamerId
getSampleData | Get WideSomaLogicData attributes
getSampleData.LongSomaLogicData | Get WideSomaLogicData attributes
getSampleData.WideSomaLogicData | Get WideSomaLogicData attributes
getSampleIdVar | Get name of sample id variable
getSequenceData | Get WideSomaLogicData attributes
getSequencesWithLargestBetweenGroupVariation | Get sequences with the largest between group variation
getUniProtKeywords | Get UniProt Keywords by AptamerId
goBiologicalProcess | GO definitions by SomaLogic AptamerId
goCellularComponent | GO definitions by SomaLogic 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 AptamerId
keggDefinitions1129 | KEGG definitions, modules, and pathways by SomaLogic AptamerId
keggModules | KEGG definitions, modules, and pathways by SomaLogic AptamerId
keggModules1129 | KEGG definitions, modules, and pathways by SomaLogic AptamerId
keggPathways | KEGG definitions, modules, and pathways by SomaLogic AptamerId
keggPathways1129 | KEGG definitions, modules, and pathways by SomaLogic AptamerId
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
setChecksum | Get WideSomaLogicData attributes
setIntensities | Get WideSomaLogicData attributes
setMetadata | Get WideSomaLogicData attributes
setSampleData | Get WideSomaLogicData attributes
setSequenceData | Get WideSomaLogicData attributes
soma2eset | Convert objects into ExpressionSets or MSnSets.
uniprotKeywords | UniProt Keywords by SomaLogic AptamerId
WideSomaLogicData | Create a WideSomaLogicData object
WideSomaLogicDataAttributes | Get WideSomaLogicData attributes
writeSampleSubmissionForm | Write a SomaLogic sample submission form
[.WideSomaLogicData | Indexing for WideSomaLogicData objects