NEWS.md

In SomaDataIO: Input/Output 'SomaScan' Data

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 :construction:

• 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 :partying_face: :champagne:

Lifting Code :rocket:

• 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 :sparkles:

• 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 :nerd_face:

• 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 :hammer:

• 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 :construction:

• 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 :tada:

• We are now on CRAN! :partying_face:

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!

SomaDataIO documentation built on April 4, 2025, 2:14 a.m.