NEWS.md

SomaDataIO 6.5.0.9000

New Functions

• Added medianNormalize() function

  • performs median normalization of study samples on soma_adat objects that have been hybridization normalized and plate scaled
  • includes validation to ensure required normalization steps have been applied
  • supports multiple reference approaches:
    • Internal reference built from study samples
    • Reference extracted from existing soma_adat object
    • External reference as a data.frame
  • supports custom grouping by multiple clinical variables

• Added reverseMedianNormalize() function

  • reverses median normalization (including ANML) that was previously applied to study samples (SampleType == "Sample")
  • designed to work with standard SomaScan deliverable ADAT files where study samples have undergone median or ANML normalization as the final sample processing step

Function and Object Improvements

• Removed restrictive file validation from read_annotations()
  • removed md5sum checksum validation and version dictionary checks resulting in misleading warnings about unknown annotations files
  • warning was often misleading, as menu annotations file updates are not always in alignment with timing of CRAN releases
  • removed getAnnoVer() function and ver_dict object
  • removed tools::md5sum import dependency

SomaDataIO 6.5.0

Function and Object Improvements

• Updated preProcessAdat() to improve clarity
  • filter.qc parameter has been renamed to filter.rowcheck
  • for backward compatibility, filter.qc is still accepted but will generate a deprecation warning and will be removed in a future version
  • removed language that discusses implication of ColCheck SeqIds not being removed from preProcessAdat() output
• Updated read_annotations() function and ver_dict object to recognize latest menu annotations files from Q3 2025

Documentation Updates

• updated statistical analysis workflow articles with clearer messaging comments around preProcessAdat()
• updated two-group and three-group analysis workflow articles to set center.scale = FALSE in preProcessAdat() to align with guidance to users for univariate analysis

Internal 🚧

• Updated dplyr verb tests to no longer explicitly test for ordering of attributes (#165)

SomaDataIO 6.4.0

New Functions

• Added updateColMeta() function

  • added utility function to update the column metadata in an ADAT to match an annotations object from read_annotations()

• Added is.AptName() to check for AptName format

  • is.apt() may return TRUE for both SeqIds and AptNames
  • wrote new function, is.AptName(), to explicitly check if a SomaScan identifier is an AptName
  • is.AptName() code and tests based on code/tests from is.SeqId()

Function and Object Improvements

• Relaxed file version requirement in read_annotations()

  • now returns warning instead of error if annotations excel file version does not match specific values

• Updated preProcessAdat() to handle missing ColCheck

  • added logic to preProcessAdat() to handle adats that are missing ColCheck in column annotation data

Documentation Updates

• Show package loading in stat workflow vignettes
  • move library() calls loading third-party packages to new code chunk that now appears in analysis workflow articles

SomaDataIO 6.3.0

New Functions

• Added preProcessAdat() function

  • added new function preProcessAdat() to filter features, filter samples, generate data QC plots of normalization scale factors by covariates, and perform standard analyte RFU transformations including log10, centering, and scaling

• Added calcOutlierMap() function

  • added calcOutlierMap() and its print and plot S3 methods, along with getOutlierIds() for identifying sample level outliers from outlier map object
  • added ggplot2 as a package dependency

Function and Object Improvements

• Added ex_clin_data object
  • a tibble object with additional sample annotation fields smoking_status and alcohol_use to demonstrate merging to a soma_adat object

Documentation Updates

• Added pre-processing vignette article

  • includes guidance on pre-processing SomaScan data for a typical analysis
  • provides an example of recommended workflow of filtering features, filtering samples, performing data QC checks, and transformations of RFU features
  • introduces usage of the preProcessAdat() function

• Improved adat ingest documentation in README

  • added comments to clarify file path input to read_adat() example in README

• Updated stat workflow articles to begin with reading in adat

  • updated data preparation chunks with comments about how to download and read in the the example_data.adat object
  • data preparation chunks now use the preProcessAdat() function for pre-processing

• Added sample annotation merging guidance

  • updated README and loading and wrangling vignette article with section including code to join the ex_clin_data object to the example_data adat

Internal 🚧

• Added helper utility functions for snapshot plot unit tests
  • added helper utility functions figure(), close_figure(), save_png(), and expect_snapshot_plot() for saving plot snapshot output to testthat/helper.R
  • added snapshot unit tests for preProcessAdat() messaging, print and QC plot output

SomaDataIO 6.2.0

New Functions

• Added calc_eLOD() function (#131)
  • calculates the estimated limit of detection (eLOD) for SeqId columns of an input soma_adat or data.frame

Bug Fixes

• Fixed crayon bug and ui_bullet() issue (#129, #130)

  • removed crayon and usethis as dependencies in favor of cli
  • fixed bug in R version 4.4.1 with ui_bullet() internal calls within loadAdatsAsList() and write_adat()

• Fixed bug in Summary.soma_adat() operations (#121)

  • these operations: min(), max(), any(), range(), etc. would return the incorrect value due to an as.matrix() conversion under the hood
  • now skips that conversion, trips a warning, and carries on
  • triggers an error if non-numerics are passed as part of the '...' outside of a soma_adat, just like Summary.data.frame()

Function and Object Improvements

• collapseAdats() now maintains Cal.Set entries of Col.Meta (#113)

  • collapsing ADATs can be problematic for the attributes, especially for large numbers of ADATs
  • collapseAdats() now attempts to smartly merge the (potentially numerous elements) Col.Meta attribute in the final object, preserving the "Cal.Set" and "ColCheck" columns in particular
  • the resulting Col.Meta attribute is a combined product of the individual ADAT elements, and the intersect of the analyte features (as is the case for the rbind() that is called)

• Updated checksums and versions for Annotations Excel files (#116)

  • updated the 7k and 11k file versions and md5sum checksums
  • now allows read_annotations() to load the individual Excel files

• Updated lift_master object to alpha sort columns

Documentation Updates

• Updated company name, license year, and maintainer (#137)

  • SomaLogic Operating Co., Inc is now Standard BioTools, Inc.
  • updated license and copyright year to 2025
  • updated package maintainer to Caleb Scheidel

• Updated article links in README, intro vignette (#123)

  • updated links to articles in README and introduction vignette to URLs to pkgdown website rather than vignette() code references
  • added clarification to above documents that articles are available on website only rather than traditional vignettes included with package

• Updates to example documentation

  • read_annotations() example documentation now points to the most recent 11k Excel annotations file
  • parseHeader() example now prints list elements separately, rather than full object, which slowed website rendering

Internal 🚧

• Updates to GitHub Action workflows

  • added rhub.yaml configuration file to comply with rhub v2
  • updated macOS version in pkgdown.yaml to macOS-14
  • added write permission to pkgdown.yaml file to enable deployment
  • changed GitHub Action R checks to MacOS and Windows only
    • ubuntu machine was taking too long to build

• Increased package test coverage

  • added unit tests for getSomaScanLiftCCC(), parseCheck() and release utilities which were previously untested
  • increased test coverage for pivotExpressionSet()

• Added missing package anchors to .Rd files (#139)

  • fixed note from remote windows check related to Rd \link{} targets missing package anchors

• Updated README badge (#109)

  • now shows 'downloads' per month over total downloads

• Fixed link in DESCRIPTION; master -> main (#107)

SomaDataIO 6.1.0 🥳 🍾

Lifting Code 🚀

• Major restructure of lift_adat() functionality (@stufield, #81, #78)

  • lift_adat() now takes a bridge = argument, replacing the anno.tbl = argument. Lifting is now performed internally for a better (and safer) user experience, without the necessity of an external annotations (Excel) file.
  • the majority of this refactoring was internal and the user should not experience a major disruption to the API.
  • much improved lifting/bridging documentation (#82)

• Added a new lifting and bridging vignette (@stufield, #77)

  • in addition to the improved lifting documentation this new vignette provides additional context, explanation, clear examples, and lifting guidance.

New Functions ✨

• is_lifted() is new and returns a boolean according to whether the signal space (RFU) has been previously lifted

• Lifting accessor function for Lin's CCC values (#88)

  • getSomaScanLiftCCC() accesses the lifting correlations between SomaScan versions for each analyte
  • returns a tibble split by sample matrix (serum or plasma)

• merge_clin() is newly exported (#80)

  • a thin wrapper that allows users to merge clinical variables to soma_adat objects easily
  • previously users had to either use the CLI merge tool or merge in clinical variables themselves with dplyr

• Newly exported ADAT "get**" helpers (#83)

  • functions to access properties of ADATs
    • getAdatVersion()
    • getSomaScanVersion()
    • getSignalSpace()
    • checkSomaScanVersion()
  • getAdatVersion() gets a new S3 method (#92)
    • this enables passing of different objects
    • namely soma_adat or list depending on the situation

• Newly exported functions that were previously internal only:

  • addAttributes()
  • addClass()
  • cleanNames()

New Vignettes 🤓

• The package README is now simplified (#35)

  • example analysis workflows are now split out into their own vignettes/articles and cross-linked in the README

• Reorganization and expansion of statistical vignettes (#35, #47)

  • moved 3 existing statistical examples from README into their own vignettes
  • resulting in four new "Statistical Workflow" vignettes/articles:
    • Binary classification via logistic regression
    • Linear regression for continuous variables
    • Two-group comparison via t-test
    • Three-group analysis ANOVA

• Added new general analysis workflow vignettes

  • articles for the pkgdown website have been built out
  • new articles on:
    • safely mapping values among variables
    • safely renaming a data frame
    • loading-and-wrangling
    • typical train and test data splits
    • beginning the FAQs and/or Coming Soon pages

• Added a new vignette describing how to use the command-line interface merge tool (#45)

  • the new CLI merge tool used to add new clinical data to existing ADAT file

Updates and Improvements 🔨

• collapseAdats() better combines HEADER information (#86)

  • certain information, e.g. PlateScale and Cal*, are better maintained in the final collapsed ADAT
  • other entries are combined by pasting into a single string
  • should result in less duplication of superfluous entries and retention of more "useful" HEADER information in the resulting (collapsed) soma_adat

• Update read_annotations() with 11k content (#85)

• Update transform() and scaleAnalytes()

  • scaleAnalytes() (internal) now skips missing references and is much more like a "step" in the recipes package
  • transform() gets edge case protection with drop = FALSE in case a single-analyte soma_adat is scaled.

• New row.names() S3 method support for soma_adat class

  • dispatched on calls to rownmaes()
  • rather than calling NextMethod() which normally would invoke data.frame, we now force the data.frame method in case there are tbl_df or grouped_df classes present that would be dispatched. Those are bypassed in favor of the data.frame because tbl_df 1) can nuke the attributes, 2) triggers a warning about adding rownames to a tibble.

• New grouped_df S3 print support for the grouped soma_adat

  • now displays Grouping information from a call to the S3 print method for soma_adat class

• New grouped_df S3 method support for soma_adat class (#66)

  • grouped_df data objects previously unsupported and were interfering with downstream S3 methods for dplyr verbs once NextMethod() was called
  • this support now ensures that the group methods are maintained, as well as the soma_adat class itself (and most importantly, with its attributes intact)

• tidyr::separate.soma_adat() S3 method was simplified (#72)

  • now uses %||% helper internally
  • expanded error messages inside stopifnot() to be more informative

• is_intact_attr() is now much quieter, signaling only when called indirectly (#71)

  • new conditional logic to silences signaling messages when called from within another function (indirectly)
  • these previously lead to confusing messages when they appear in wrappers, where is_intact_attr() can be, sometimes deeply, nested in the call stack

• Development and improvements to the pkgdown website

  • added new links and improved clarity in YAML
  • added new logo at footer
  • restyled side bar for easier hyperlinking and getting help
  • clicking on the SomaLogic logo in the GitHub README now links to the pkgdown website
  • new "Coming Soon" drop-down section in the website header to let users know about active progress (but not yet ready for external publication)

• SomaDataIO no longer depends on desc package

  • to generate the README.md

Internal 🚧

• Internal rowname helpers were upgraded

  • they now use internal cross-functions as originally intended to avoid redundancy, efficiency, and improved debugging

• sysdata.rda no longer contains non-exported functions (#59)

  • new internal helper functions:
    • convertColMeta()
    • genRowNames()
    • parseCheck()
    • syncColMeta()
    • scaleAnalytes()

• Bug-fix for corner-case writing a single-analyte ADAT (#51)

  • RFU values are rounded to 1 decimal place when written by write_adat(), via a call to apply(), which expects a 2-dim object when replacing those values.
  • write_adat() no longer uses apply() and instead converts the entire RFU data frame to a matrix (maintains original dimensions), and use vectorized format conversion via sprintf()
  • in theory this should be faster because sprintf() is only called once on a long vector, rather than 1000s of times on shorter vectors (inside apply()).

• Fixed missing closing parenthesis in SomaScanObjects.R (thanks @Hijinx725!, #40)

SomaDataIO 6.0.0 🎉

• We are now on CRAN! 🥳

New changes

• New clinical data merge CLI tool (@stufield, #25)

  • Rscript --vanilla merge_clin.R for merging clinical variables into existing *.adat SomaScan data files
  • added 2 new example meta.csv and meta2.csv files to run examples with random data but with valid index keys
  • see dir(system.file("cli", "merge", package = "SomaDataIO"))

• Package data objects (@stufield, #32)

  • example_data.adat was reduced in size to n = 10 samples (from 192) to conform to CRAN size requirements (< 5MB)
  • the current file was renamed example_data10.adat to reflect this change
  • this likely has far-reaching consequences for users who access this flat file via system.file()
  • the example_data object itself however remains true to its original file (https://github.com/SomaLogic/SomaLogic-Data/blob/master/example_data.adat)
  • the directory location inst/example/ was renamed inst/extdata/ to conform to CRAN package standard naming conventions
  • the file single_sample.adat was removed from package data as it is now redundant (however still used in unit testing)
  • SomaDataObjects was renamed and is now SomaScanObjects

• Gradual deprecation (@stufield)

  • read.adat() is now soft-deprecated; please use read_adat() instead
  • lifecycle for soft-deprecated warn() -> stop() for functions that have been been soft deprecated since v5.0.0
    • getSomamers()
    • getSomamerData()
    • meltExpressionSet()

• New S3 print method default (@stufield)

  • tibble has new max_extra_cols = argument, which is set to 6 for the print.soma_adat method

• New S3 merge method (@stufield, #31)

  • calling base::merge() on a soma_adat is strongly discouraged
  • we now redirect users to use dplyr::*_join() alternatives which are designed to preserve soma_adat attributes

• Code hardening for prepHeaderMeta() (@stufield)

  • some ADATs do not have CreatedDate and CreatedBy in the HEADER entry. This currently breaks the writer
  • simplified to make more robust but also refactor to be more convenient (for abnormal ADATs not generated by standard SomaScan processing)
  • CreatedDateHistory was removed as an entry from written ADATs
  • CreatedByHistory was combined and dated for written ADATs
  • NULL behavior remains if keys are missing
  • CreatedBy and CreatedDate will be generated either as new entries or over-written as appropriate

• Numerous non-user-facing (API) changes internal package maintenance, efficiency, and structural upgrades were included

SomaDataIO 5.3.1

• Bug-fix release related to write_adat():

  • fixed bug in write_adat() that resulted from adding/removing clinical (non-SomaScan) variables to an ADAT. Export via write_adat() resulted in a broken ADAT file (@stufield, #18)
  • write_adat() now has much higher fidelity to original text file (*.adat) in full-cycle read-write-read operations; particularly in presence of bangs (!) in the Header section and in floating point decimals in the ?Col.Meta section
  • write_adat() no longer converts commas (,) to semi-colons (;) in the ?Col.Meta block (originally introduced to avoid cell alignment issues in *.csv formats)
  • write_adat() no longer concatenates written ADATs, when writing to the same file. Data is over-written to file to avoid mangled ADATs resulting from re-writing to the same connection and to match the default behavior of write.table(), write.csv(), etc.

• read_adat() now has more consistent character type the Barcode2 variable in standard ADATs, now forces character class, does not allow R's read.delim() to "guess" the type

• Decreased dependency of magrittr pipes (%>%) in favor of the native R pipe (|>). As a result the package now depends on R >= 4.1.0

  • SomaDataIO will continue to re-export magrittr pipes for backward compatibility, but this should not be considered permanent. Please code accordingly

• Migration to the default branch in GitHub from master -> main (@stufield, #19)

• Numerous non-user-facing (API) changes internal package maintenance, efficiency, and structural upgrades were included

SomaDataIO 5.3.0

• Upgrades primarily from improvements to SomaLogic internal code base, including: (@stufield)

  • general reduction on external package dependency to improve code stability
  • internal usage of base R alternatives to the readr package for parsing and importing ADATs (e.g. read.delim() over readr::read_delim()). This is mostly for code simplification, but can often result in marked speed improvements. As the SomaScan plex size increases, this speed improvement will become more important.
  • parseHeader() was dramatically simplified, now reading in lines 20L at a time until the RFU block is reached. In addition, once the block is reached, all header lines are read-in once and indexed (as opposed to line-by-line).
  • read_adat() now specifies column types via colClasses = which for the majority of the ADAT is type double for the RFU columns. This should dramatically improve speed of ingest.
  • write_adat() was simplified internally, with fewer nested apply and for-loops.
  • encoding for all input/output (I/O) is assumed to be UTF-8.

• New getAnalytes() S3 method for class recipe from the recipes package.

• New loadAdatsAsList() to load multiple ADAT files in a single call and optionally collapse them into a single data frame (@stufield, #8).

• New getTargetNames() function to map ADAT seq.XXXX.XX names to corresponding protein targets from the annotations table

SomaDataIO 5.2.0

• SomaLogic Inc. is now SomaLogic Operating Co. Inc.

• Added new documentation regarding Col.Meta (@stufield, #12).

  • documentation around column meta data, row meta data, where they are found in an ADAT, and how to access them.

• Research Use Only ("RUO") language was added to the README (@stufield, #10).

• Numerous internal code improvements from SomaLogic code-base (@stufield)

  • the consisted of reducing usage of external dependencies, e.g. using stop() over ui_stop() and warning() over ui_warn(), using usethis, cli, and crayon shims aliases.
  • package uses purrr very selectively and no longer uses stringr.
  • using base R alternatives in favor of increased stability for underlying, non-user-facing code.

• New lift_adat() was added to provided 'lifting' functionality (@stufield, #11)

  • provides mechanism to convert RFU space between SomaScan versions (e.g. v4.1 -> v4.0).
  • added new S3 transform.soma_adat() method which simplifies linear scaling of soma_adat columns (analytes).
  • uses an "Annotations file" (Excel) as source of scalars for transformation.

• Minor improvements and updates to the README.Rmd (@stufield, #7)

  • fixed a broken adat2eSet() link in README (#5).
  • clearer text to the README regarding Biobase installation.
  • added new links to external Bioconductor website in installation section of README.
  • new pkgdown and links to Issues (#4).
  • SomaLogic logo was added to README.
  • a lifecycle ("maturing") badge was added.

• Startup message was improved with dynamic width (@stufield).

• New locateSeqId() function to pull out SeqId regex. (@stufield).

• New read_annotations() function (@stufield, #2)

  • new function to parse/import SomaLogic annotations files (*.xlsx).

SomaDataIO 5.1.0

• New set_rn() drop-in replacement for magrittr::set_rownames()

• getFeatures() was renamed to be less ambiguous and better align with internal SomaLogic code usage. Now use getAnalytes() (@stufield)

• getFeatureData() was also renamed to getAnalyteInfo() (@stufield)

• various upgrades as required by code changes in external package dependencies, e.g. tidyverse.

• new alias for read_adat(), read.adat(), for backward compatibility to previous versions of SomaDataIO (@stufield)

SomaDataIO 5.0.0

• Initial public release to GitHub!