Package: SomaDataIO 6.1.0.9000

Stu Field

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, cre], SomaLogic Operating Co., Inc. [cph, fnd]

SomaDataIO_6.1.0.9000.tar.gz
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SomaDataIO.pdf |SomaDataIO.html✨
SomaDataIO/json (API)
NEWS

# 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

Datasets:

ex_analytes - Example Data and Objects
ex_anno_tbl - 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

70 exports 25 stars 2.93 score 49 dependencies 101 scripts 484 downloads

Last updated 4 months agofrom:95867135f0. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 13 2024
R-4.5-win	NOTE	Sep 13 2024
R-4.5-linux	NOTE	Sep 13 2024
R-4.4-win	OK	Sep 13 2024
R-4.4-mac	OK	Sep 13 2024
R-4.3-win	OK	Sep 13 2024
R-4.3-mac	OK	Sep 13 2024

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

Dependencies:askpass cellranger cli clipr cpp11 crayon credentials curl desc dplyr fansi fs generics gert gh gitcreds glue hms httr2 ini jsonlite lifecycle magrittr openssl pillar pkgconfig prettyunits progress purrr R6 rappdirs readxl rematch rlang rprojroot rstudioapi stringi stringr sys tibble tidyr tidyselect usethis utf8 vctrs whisker withr yaml zip

Introduction to SomaDataIO

Rendered fromSomaDataIO.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2024-05-15
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
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
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
Merge Clinical Data into SomaScan	merge_clin
Common Parameters in 'SomaDataIO'	params
SomaLogic ADAT parser	parseHeader
Convert to Long Format	meltExpressionSet pivotExpressionSet
Read (Load) SomaLogic ADATs	is.soma_adat read.adat read_adat
Import a SomaLogic Annotations File	read_annotations
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.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_target_names SomaScanObjects
Scale Transform 'soma_adat' Columns/Rows	transform transform.soma_adat
Write an ADAT to File	write_adat