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:
SomaDataIO_6.1.0.9000.tar.gz
SomaDataIO_6.1.0.9000.zip(r-4.5)SomaDataIO_6.1.0.9000.zip(r-4.4)SomaDataIO_6.1.0.9000.zip(r-4.3)
SomaDataIO_6.1.0.9000.tgz(r-4.4-any)SomaDataIO_6.1.0.9000.tgz(r-4.3-any)
SomaDataIO_6.1.0.9000.tar.gz(r-4.5-noble)SomaDataIO_6.1.0.9000.tar.gz(r-4.4-noble)
SomaDataIO_6.1.0.9000.tgz(r-4.4-emscripten)SomaDataIO_6.1.0.9000.tgz(r-4.3-emscripten)
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
- 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
adatproteomicsproteomics-data-analysissomascan
Last updated 2 months agofrom:4714fae84d. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 25 2024 |
| R-4.5-win | NOTE | Oct 25 2024 |
| R-4.5-linux | NOTE | Oct 25 2024 |
| R-4.4-win | OK | Oct 25 2024 |
| R-4.4-mac | OK | Oct 25 2024 |
| R-4.3-win | OK | Oct 25 2024 |
| R-4.3-mac | OK | Oct 25 2024 |
Exports:%>%adat2eSetadd_rowidaddAttributesaddClassanti_joinantilogapt2seqidarrangecalc_eLODcheckSomaScanVersioncleanNamescol2rncollapseAdatscountdiffAdatsfilterfull_joingetAdatVersiongetAnalyteInfogetAnalytesgetFeatureDatagetFeaturesgetMetagetSeqIdgetSeqIdMatchesgetSignalSpacegetSomamerDatagetSomamersgetSomaScanLiftCCCgetSomaScanVersiongetTargetNamesgroup_byhas_rninner_joinis_intact_attris_liftedis_seqFormatis.aptis.intact.attributesis.SeqIdis.soma_adatleft_joinlift_adatloadAdatsAsListlocateSeqIdmatchSeqIdsmeltExpressionSetmerge_clinmutateparseHeaderpivotExpressionSetread_adatread_annotationsread.adatregexSeqIdrenameright_joinrm_rnrn2colsample_fracsample_nsemi_joinseparateseqid2aptset_rnsliceslice_sampleungroupunitewrite_adat
Dependencies:cellrangerclicpp11crayondplyrfansigenericsgluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readxlrematchrlangstringistringrtibbletidyrtidyselectutf8vctrswithr
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 |
| 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 |
