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Load an ADAT

Load RFU (feature) data loaded into (and out of) an R session.

ADAT Manipulation

Functions that allow filtering, wrangling, and subset selection of ADAT objects.

getSeqId() regexSeqId() locateSeqId() seqid2apt() apt2seqid() is.apt() is.SeqId() matchSeqIds() getSeqIdMatches()
Working with SomaLogic SeqIds
is_seqFormat()
Test AptName Format
getAnalyteInfo() getTargetNames() getFeatureData()
Get Analyte Annotation Information
getAnalytes() getMeta() getFeatures()
Get Analytes
diffAdats()
Diff Two ADAT Objects
merge_clin()
Merge Clinical Data into SomaScan

Transform Between SomaScan Versions

Functionality required to bridge between SomaScan versions, e.g. 11k -> 7k, sometimes referred to as “lifting”.

lift_adat() is_lifted()
Lift an ADAT Between Assay Versions
read_annotations()
Import a SomaLogic Annotations File
transform(<soma_adat>)
Scale Transform soma_adat Columns/Rows
getAdatVersion() getSomaScanVersion() getSignalSpace() checkSomaScanVersion() getSomaScanLiftCCC()
Helpers to Extract Information from an ADAT

Expression Data

Functions to convert objects to those familiar with expression data.

adat2eSet()
Convert ADAT to ExpressionSet Object
pivotExpressionSet() meltExpressionSet()
Convert to Long Format

Helpers

Accessor functions to add, modify, or retreive attribute information. Typically used internally but are exported for user convenience.

addAttributes()
Add Attributes to soma_adat Objects
addClass()
Add a Class to an Object
cleanNames()
Clean Up Character String
getAdatVersion() getSomaScanVersion() getSignalSpace() checkSomaScanVersion() getSomaScanLiftCCC()
Helpers to Extract Information from an ADAT

Data Objects

Objects provided with SomaDataIO.

Parameters

Common parameter arguments to functions in SomaDataIO.

params
Common Parameters in SomaDataIO

Deprecated

Functions that have been deprecated (sunset) in the current SomaDataIO release.

SomaDataIO-deprecated getSomamers getSomamerData
Deprecated function(s) of the SomaDataIO package