Package index • SomaDataIO

Load an ADAT

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

read_adat() read.adat() is.soma_adat() superseded: Read (Load) SomaLogic ADATs

write_adat(): Write an ADAT to File

print(<soma_adat>) summary(<soma_adat>) `[`(<soma_adat>) `$`(<soma_adat>) `[[`(<soma_adat>) `[<-`(<soma_adat>) `$<-`(<soma_adat>) `[[<-`(<soma_adat>) median(<soma_adat>): The soma_adat Class and S3 Methods

loadAdatsAsList() collapseAdats(): Load ADAT files as a list

parseHeader(): SomaLogic ADAT parser

rn2col() col2rn() has_rn() rm_rn() set_rn() add_rowid(): Helpers for Working With Row Names

Col.Meta colmeta annotations rowmeta: Analyte Annotations, Col.Meta, and Row Info

is_intact_attr() is.intact.attributes() superseded: Are Attributes Intact?

Math(<soma_adat>) antilog() Ops(<soma_adat>) Summary(<soma_adat>) `==`(<soma_adat>): Group Generics for soma_adat Class Objects

reexports count rename slice_sample slice sample_frac sample_n filter mutate arrange group_by ungroup left_join anti_join full_join inner_join semi_join right_join unite separate: Objects exported from other packages

ADAT Manipulation

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

getSeqId() regexSeqId() locateSeqId() seqid2apt() apt2seqid() is.apt() is.SeqId() is.AptName() 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

preProcessAdat(): Pre-Process an ADAT Object for Analysis

updateColMeta(): Update Col.Meta Attribute to Match Annotations Object

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 Summaries

Functions to assist with summarizing SOMAmer RFU values.

calc_eLOD(): Calculate Estimated Limit of Detection (eLOD)

Data Objects

Objects provided with SomaDataIO.

SomaScanObjects example_data ex_analytes ex_anno_tbl ex_target_names ex_clin_data: Example Data and Objects

Parameters

Common parameter arguments to functions in SomaDataIO.

params: Common Parameters in SomaDataIO

Plotting

Functions to assist with plotting information from ADAT objects.

calcOutlierMap() print(<outlier_map>): Calculate MAD Outlier Map

getOutlierIds(): Get Flagged Ids From MAD Outlier Map

plot(<Map>): Plot Image Maps

Deprecated

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

SomaDataIO-deprecated getSomamers getSomamerData superseded: Deprecated function(s) of the SomaDataIO package