Package: SomaDataIO 6.6.1

Caleb Scheidel

SomaDataIO: Input/Output 'SomaScan' Data

Load and export 'SomaScan' data via the 'SomaLogic Operating Co., Inc.' structured text file called an ADAT ('*.adat'). For file format see <https://github.com/SomaLogic/SomaLogic-Data/blob/main/README.md>. The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.

Authors:Stu Field [aut], Caleb Scheidel [cre], SomaLogic Operating Co., Inc. [cph, fnd]

SomaDataIO_6.6.1.tar.gz
SomaDataIO_6.6.1.zip(r-4.7)SomaDataIO_6.6.1.zip(r-4.6)SomaDataIO_6.6.1.zip(r-4.5)
SomaDataIO_6.6.1.tgz(r-4.6-any)SomaDataIO_6.6.1.tgz(r-4.5-any)
SomaDataIO_6.6.1.tar.gz(r-4.7-any)SomaDataIO_6.6.1.tar.gz(r-4.6-any)
SomaDataIO_6.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SomaDataIO/json (API)

# Install 'SomaDataIO' in R:

install.packages('SomaDataIO', repos = c('https://somalogic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/somalogic/somadataio/issues

Pkgdown/docs site:https://somalogic.github.io

Datasets:

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
example_data - Example Data and Objects

On CRAN:

adat proteomics proteomics-data-analysis somascan

8.79 score 29 stars 2 packages 152 scripts 1.0k downloads 78 exports 36 dependencies

Last updated from:eb4bc728a4. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	229
source / vignettes	OK	222
linux-release-x86_64	OK	219
macos-release-arm64	OK	220
macos-oldrel-arm64	OK	204
windows-devel	OK	163
windows-release	OK	176
windows-oldrel	OK	185
wasm-release	OK	135

Exports:%>%adat2eSet add_rowid addAttributes addClass anti_join antilog apt2seqid arrange calc_eLOD calcOutlierMap checkSomaScanVersion cleanNames col2rn collapseAdats count diffAdats filter full_join getAdatVersion getAnalyteInfo getAnalytes getFeatureData getFeatures getMeta getOutlierIds getSeqId getSeqIdMatches getSignalSpace getSomamerData getSomamers getSomaScanLiftCCC getSomaScanVersion getTargetNames group_by has_rn inner_join is_intact_attr is_lifted is_seqFormat is.apt is.AptName is.intact.attributes is.SeqId is.soma_adat left_join lift_adat loadAdatsAsList locateSeqId matchSeqIds medianNormalize meltExpressionSet merge_clin mutate parseHeader pivotExpressionSet preProcessAdat read_adat read_annotations read.adat regexSeqId rename reverseMedianNormalize right_join rm_rn rn2col sample_frac sample_n semi_join separate seqid2apt set_rn slice slice_sample ungroup unite updateColMeta write_adat

Dependencies:cellranger cli cpp11 crayon dplyr farver generics ggplot2 glue gtable hms isoband labeling lifecycle magrittr pillar pkgconfig prettyunits progress purrr R6 RColorBrewer readxl rematch rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Introduction to SomaDataIO

Main Features (I/O) | Workflows and Analysis | MIT LICENSE

Rendered fromSomaDataIO.Rmdusingknitr::rmarkdown

Last update: 2026-02-06
Started: 2020-09-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Helpers to Extract Information from an ADAT	adat-helpers checkSomaScanVersion getAdatVersion getSignalSpace getSomaScanLiftCCC getSomaScanVersion
Convert ADAT to ExpressionSet Object	adat2eSet
Add Attributes to 'soma_adat' Objects	addAttributes
Add a Class to an Object	addClass
Calculate Estimated Limit of Detection (eLOD)	calc_eLOD
Calculate MAD Outlier Map	calcOutlierMap print.outlier_map
Clean Up Character String	cleanNames
Analyte Annotations, Col.Meta, and Row Info	annotations Col.Meta colmeta rowmeta
Diff Two ADAT Objects	diffAdats
Get Analyte Annotation Information	getAnalyteInfo getFeatureData getTargetNames
Get Analytes	getAnalytes getFeatures getMeta
Get Flagged Ids From MAD Outlier Map	getOutlierIds
Group Generics for 'soma_adat' Class Objects	==.soma_adat antilog groupGenerics Math.soma_adat Ops.soma_adat Summary.soma_adat
Are Attributes Intact?	is.intact.attributes is_intact_attr
Test 'AptName' Format	is_seqFormat
Lift an ADAT Between Assay Versions	is_lifted lift_adat
Load ADAT files as a list	collapseAdats loadAdatsAsList
Perform Median Normalization on Study Samples	medianNormalize
Merge Clinical Data into SomaScan	merge_clin
Common Parameters in 'SomaDataIO'	params
SomaLogic ADAT parser	parseHeader
Convert to Long Format	meltExpressionSet pivotExpressionSet
Plot Image Maps	plot.Map
Pre-Process an ADAT Object for Analysis	preProcessAdat
Read (Load) SomaLogic ADATs	is.soma_adat read.adat read_adat
Import a SomaLogic Annotations File	read_annotations
Reverse Median Normalization from Study Samples	reverseMedianNormalize
Helpers for Working With Row Names	add_rowid col2rn has_rn rm_rn rn2col rownames set_rn
Working with SomaLogic SeqIds	apt2seqid getSeqId getSeqIdMatches is.apt is.AptName is.SeqId locateSeqId matchSeqIds regexSeqId SeqId seqid2apt
The 'soma_adat' Class and S3 Methods	$.soma_adat $<-.soma_adat median.soma_adat print.soma_adat soma_adat summary.soma_adat [.soma_adat [<-.soma_adat [[.soma_adat [[<-.soma_adat
Deprecated function(s) of the 'SomaDataIO' package	getSomamerData getSomamers SomaDataIO-deprecated
Example Data and Objects	example_data ex_analytes ex_anno_tbl ex_clin_data ex_target_names SomaScanObjects
Scale Transform 'soma_adat' Columns/Rows	transform transform.soma_adat
Update Col.Meta Attribute to Match Annotations Object	updateColMeta
Write an ADAT to File	write_adat