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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!

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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