Functionality to Read and Manipulate SomaLogic ADAT files


[Up] [Top]

Documentation for package ‘readat’ version 1.0.0

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
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
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
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