# Input/Output 'SomaScan' Data

## Documentation for package ‘SomaDataIO’ version 6.6.0

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

## 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
calcOutlierMap | Calculate MAD Outlier Map
calc_eLOD | Calculate Estimated Limit of Detection (eLOD)
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_clin_data | 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
getOutlierIds | Get Flagged Ids From MAD Outlier Map
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.AptName | 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
medianNormalize | Perform Median Normalization on Study Samples
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
plot.Map | Plot Image Maps
preProcessAdat | Pre-Process an ADAT Object for Analysis
print.outlier_map | Calculate MAD Outlier Map
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
reverseMedianNormalize | Reverse Median Normalization from Study Samples
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
updateColMeta | Update Col.Meta Attribute to Match Annotations Object
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