NEWS

OlinkAnalyze 4.0.1 (2024-09-24)

Minor Changes

larger rds files used for unit tests have been excluded from build to abide by CRAN size limitations (#462, @kathy-nevola)

OlinkAnalyze 4.0.0

Major Changes

olink_normalization can now be used for bridging Explore 3072 data to Explore HT data (#453, #452, #439, #449, #447,#446, #441, #440, #434, #422, #436, #435 @klevdiamanti, @kathy-nevola, @kristynchin-olink, @dtopouza, @amrita-kar, @MasoumehSheikh)
olink_normalization has undergone major changes to improve speed, reproducibility, and extending functionality (#418, @klevdiamanti, @kristynchin-olink, @MasoumehSheikh)

Minor Changes

New tutorial has been added to explain and support Explore 3072 to Explore HT bridging (#448, #428, #427, #426, #425, #424, #423, @kristynchin-olink, @boxizhang, @dtopouza, @kathy-nevola, @MasoumehSheikh)
Update FAQ links in tutorials with queries links (#451, @kathy-nevola)
Decrease package size on Mac and Linux (#445, @kathy-nevola)
Removed redundant information from overview vignette (#458, @kathy-nevola)

Bug Fixes

Add support back for files with quotes to read_NPX (#431 @kathy-nevola)

OlinkAnalyze 3.9.1

Bug Fix

Extra set of parentheses removed from vignette (#430, @kathy-nevola)

OlinkAnalyze 3.9.0

Minor Changes

Explore HT recommended bridging samples have been added to Introduction to Bridging tutorial (#409, @kathy-nevola)
Support for CSVs with SampleQC column was added to read_NPX (#406, @kathy-nevola)
Support for Olink Analyze Export parquets was added to read_NPX (#408, @kathy-nevola)
Quantitative value csvs will now give a warning about limited support for Quant data (#406, @kathy-nevola)
Instructions for importing multiple NPX files has been added to the overview tutorial (#403, @dtopouza)
Additional background information was added to the LOD tutorial to clarify how LOD is calculated from counts (#404, @kathy-nevola)
LOD can now be calculated using fixed LOD, negative controls, or both methods (#390, @kathy-nevola)
An error message will now appear when running anova and control assays are present (#416, @dtopouza)
Danai Topouza's role has been changed from contributor to author (#415, @kathy-nevola)

Bug Fixes

URLs in tutorials will now direct to updated olink.com locations (#402, @kathy-nevola)
Instructions to export parquet files with LOD have been updated (#408, @kathy-nevola)
removed scale_name argument when ggplot2 3.5+ is installed (#421, @kathy-nevola)

OlinkAnalyze 3.8.2 (2024-06-27)

Bug Fixes

update to URL hyperlink in LOD tutorial to include https
data with Plate_LQL and PlateLQL columns in long format will now be supported (#392, @klevdiamanti)

OlinkAnalyze 3.8.1

Bug Fixes

update to outdated URL in LOD tutorial

Minor Changes

Function support for calculating LOD for Explore data (#355, @kathy-nevola, @klevdiamanti, @leiliuC)
Tutorial and documentation for calculating LOD for Explore data (#364, @MasoumehSheikh, @kristynchin-olink, #388, @kathy-nevola, @amrita-kar)
Addition of Danai Topouza as contributor and Kristyn Chin as author (previously contributor) (#365, @kathy-nevola)

Bug Fixes

Removed outdated reference to NPX Manager (#354, @dtopouza)
Removed mention of Welch's t-test in Mann Whitney documentation (#354, @dtopouza)
Assays that include apostrophes will now be read in correctly from long format csvs (#381, @kathy-nevola)

OlinkAnalyze 3.7.0 (2024-02-22)

Minor Changes

Support for Explore 3072 data in parquet form added (#327, @kathy-nevola, @klevdiamanti)
Support for pathway enrichment when LOD is not present added (#329, @kathy-nevola)
Clarification to remove controls when selecting bridging samples added in bridging tutorial (#330, @kathy-nevola)
Addition of Kristyn Chin as contributor (#331, @kathy-nevola)
Addition of URLs and Contact information in Description (#331, @kathy-nevola)

OlinkAnalyze 3.6.2 (2024-01-13)

Bug Fixes

Packages in Suggest field are now called conditionally in vignettes, tests, and examples. (#319, @kathy-nevola)
read_NPX will now work with Target 96 data that does not contain "Target 96" in the panel name (#320, @kathy-nevola)
olink_lmer will no longer require the presence of an Index column in the data (#321, @kathy-nevola)
corrected examples for subset normalization (#312 @kathy-nevola)
added additional information on example data to outlier vignette (#313 @kathy-nevola)
clarified documentation for longitudinal randomization (#314 @kathy-nevola)
corrected warning message for olink_ordinalRegression (#296 @boxizhang)

OlinkAnalyze 3.6.1

Minor Changes

Install package Matrix from source in CI. (#299 @klevdiamanti, @AskPascal)

OlinkAnalyze 3.6.0 (2023-11-03)

Minor Changes

Plate LOD will be chosen over Max LOD when both are present (#288, @kathy-nevola)
Data from NPX Signature 1.8+ is now supported by read_NPX when in long format csv (#293, @Orbmac, @kathy-nevola)
olink_pca_plot will now be faster (#289, @MasoumehSheikh)

Bug Fixes

olink_normalization and related function will now compare normalization strategy by assay (#291, klevdiamanti)
Excluded assays will not cause warnings in olink_normalization (#291, klevdiamanti)
olink_pca_plot will now show the same label and text for point when SampleID is numeric (#289, @MasoumehSheikh)

OlinkAnalyze 3.5.1 (2023-08-08)

Bug Fixes

read_NPX will now support additional formats of parquet files

OlinkAnalyze 3.5.0

Minor Changes

read_NPX will now detect and import Flex excel files in wide format (@kathy-nevola, #234)
Add example of bridge samples selector and minor updates for clarity to Intro to bridging vignette (@Orbmac, @kathy-nevola, #260)
Increase plate randomizer unit test coverage (@amrita-kar, #264)
Add support for parquet files in read_NPX (@kathy-nevola, #265, @klevdiamanti, #270)
Add support for alternative forms of LOD including Max and Plate LOD (@kathy-nevola, #267)
Add support for SampleQC column (alternative to QC_Warning) (@kathy-nevola, #267, @MasoumehSheikhi, @268)
Add support for plate randomization with variable control numbers (@kathy-nevola, @AskPascal, #269)
Controls can now be randomized across the plate with olink_plate_randomizer (@kathy-nevola, @AskPascal, #269)
Minor updates for clarity to Plate Randomization vignette (@kathy-nevola, @AskPascal, #269)
Change formatting for long format Target CSVs to match excel (@kathy-nevola, #273)

Bug Fixes

Project name is now consistent and generic throughout bridging vignette (@kathy-nevola, #257)
Estimate is now included in output when Paired Mann-Whitney U test is performed (@boxizhang, #259)

OlinkAnalyze 3.4.1 (2023-05-08)

Bug Fixes

Skip PCA snapshot tests in R version > 4.2.3 (@AskPascal, #254)
Bridge selector will now return all samples when requesting max number of samples based on missing frequency (@klevdiamanti, #252)
Fixed unit tests to expect NA as logical instead of "NA" as character (@MasoumehSheikhi, #250)

OlinkAnalyze 3.4.0 (2023-04-26)

Minor Changes

User can now specify label for proteins in olink_heatmap_plot() (@simfor, #228)
Updates to unit test and CI based on dependency changes (@AskPascal, #231, #236, #240)
Addition of normalization functions to simplify bridge, subset, and multi-batch normalization (@klevdiamanti, #201)
Introduction to bridging vignette added (@leiliuC, @kathy-nevola, #174)
Plate Randomization vignette added (@boxizhang, #241)
Outlier Exclusion vignette added (@kathy-nevola, #229)
Added Lei Conze as author (@kathy-nevola, #246)
Addition of citation (@kathy-nevola, #246)

Bug Fixes

Update to olink_wilcox documentation and UniProt description in documentation has been corrected (@boxizhang, #235)

OlinkAnalyze 3.3.1 (2023-02-27)

Bug Fixes

olink_pathway_enrichment now prints a message when there are non matching names when using method = "ORA" (@MasoumehSheikhi, #222)
olink_pca_plot will now generate PCA when data is missing from the first OlinkID (@kathy-nevola, #221)
read_NPX now supports csv files with Sample_Type column but not ExploreVersion column (@klevdiamanti, #220)
extra columns in input file will no longer result in a warning message (@kathy-nevola, #223)

OlinkAnalyze 3.3.0 (2023-01-24)

Minor Changes

Support for additional versions of Olink data - Read_NPX now supports a wider range of Olink data types (@AskPascal, @kathy-nevola, #207, #208, #211, #216)
Automatic support for normalizing 2 datasets with different column configurations - olink_normalization will now automatically add missing columns to datasets (filled NA) to allow data with different configurations to be more easily normalized together (@kathy-nevola, #212)
Automatic checking that datasets used the same normalization method before bridging - Datasets that were normalized with different methods (different values in normalization column) will now warn before performing normalization (@klevdiamanti, #210)

Bug Fixes

Data with '#' in SampleID column is now supported (@AskPascal, #208)
PCA can now be generated when indices are not consistent across SampleIDs (@amrita-kar, #206)

OlinkAnalyze 3.2.2 (2022-11-15)

Bug Fixes

remove www. from links in vignette to prevent rerouting of URL (@kathy-nevola, #188)
update set_plot_theme() to use linewidth instead of size per ggplot2 3.4

OlinkAnalyze 3.2.1

Bug Fixes

Change in unit test to write to temporary directory (@AskPascal, #181)

OlinkAnalyze 3.2.0 (2022-11-01)

Minor Changes

Addition of functions to perform Uniform Manifold Approximation and Projection (UMAP) dimensional reduction and plots (@simfor, #139)
Add additional install methods to Readme (@AskPascal, #153)
ggrepel can now be disabled when outlier lines are present in the PCA plot (@klevdiamanti, #158)
Long running unit tests are now skipped on CRAN (@AskPascal, #163)
Internal functions were added to read_NPX to support future development (@klevdiamanti, #167)
CI workflows were refactored to utilize external actions (@AskPascal, #169)
Read_NPX will now warn the user when NAs are detected in the NPX column (@AskPascal, #170)
Friedman test interface and documentation was updated to be more intuitive (@boxizhang, #171)

Bug fixes

Pathway enrichment p-values are now in the correct order when plotting (@klevdiamanti, #164)
PCAs now behave the same with any locale (@AskPascal, #173)
Read_NPX now accepts either Panel_Version or Panel_Lot_Nr in input files (@klevdiamanti, #156)
Assays that only have NPX = NA will now be excluded from all analyses and figures (@simfor, @kathy-nevola, @AskPascal, #176)
Refactor code to use tidyselect::all_of() in recommended way (@AskPascal, #177)
vdiffr based unit tests were reactivated (@AskPascal, #172)

OlinkAnalyze 3.1.0 (2022-06-10)

Minor Changes

Non-parametric functions are now available (@boxizhang, #114, #142)
Updated installation instructions to reflect CRAN acceptance (@kathy-nevola, #107)
Zipped files from MyData can now be used as input for read_NPX (@klevdiamanti, #115)
LME and ANOVA formulas can now be customized (@jrguess, #120)
Pathway enrichment functions and visualizations are now available (@kathy-nevola, #125)
Heatmaps can now be generated (@Orbmac, $127)
olink_boxplot function now has significance bars and stars (@boxizhang, #132)
PCA preprocessing was moved to internal function (@simfor, #133)
olink_plate_randomizer will now return a warning if there are duplicate SampleIDs or if SubjectColumn is missing (@kristianHoden, #146)
olink_plate_randomizer can now keep studies together on plates (@kristianHoden, #146)
Added Masoumeh Sheikhi and Boxi Zhang as authors
Added Kristian Hodén as contributor

Bug Fixes

olink_pca_plot by Panel will now show correct colors when a variable is missing (@MasoumehSheikhi, Issue #117, Commit 0f2f157)
olink_ttest will now return a warning message if an assay has less than 2 datapoints in a group. (@marisand, #110)
LMER class is now checked using inherits (@MasoumehSheikhi, #134)
License was corrected to AGPL-3 (@Orbmac, #138)
Correct output type of olink_dist_plot in vignette to ggplot object (@kathy-nevola, Issue #112, #141)
Previously called "intensity normalization" has been clarified as a special type of subset normalization and an example has been added to the documentation and vignette (@Orbmac, #144)

OlinkAnalyze 3.0.0 (2022-02-10)

Major Changes

displayPlateDistributions and displayPlateLayout names were updated to olink_displayPlateDistributions and olink_displayPlateLayout (@simfor, #98)

Minor Changes

Update CI to Ubuntu 20.04 (@AskPascal, #97)
olink_bridgeselector will now give an error if less than n (number of) bridge samples can be selected based on set sampleMissingFreq (@marisand, #100)
update return value documentation for all functions to specify columns and class of output (@kathy-nevola, #102)
replaced or removed cat/print with message/stop so messages printed to the console can be suppressed (@jrguess, #103)

Bugfixes

fixed spelling mistakes in documentation (@kathy-nevola, #92)
updated DESCRIPTION to fit CRAN specification (@kathy-nevola, #94)
change T/F to TRUE/FALSE for stability (@AskPascal, #96)
updated documentation to olink_plate_randomizer, olink_displayPlateDistributions and olink_displayPlateLayout to link related functions and clarify olink_plate_randomizer documentation (@simfor, #98)
fixed keywords in documentation (@kathy-nevola, #99)

OlinkAnalyze 2.0.1

Bug Fixes

Remove hexagon from Readme (@kathy-nevola, #86)
Replace OlinkAnalyze with Olink® Analyze (@kathy-nevola, #86)
Add Ola Caster to author list
Update documentation to change olinkR to Olink Analyze (@jrguess, #89)

OlinkAnalyze 2.0.0

Major Changes

Package is in the process of being submitted to CRAN
Added ability to prevent OlinkAnalyze from loading fonts and setting to themes (@OlaCaster, #73)
Decreased the size of npx_data1 and npx_data2 to 2 panels instead of 12 (@kathy-nevola, #76)
Updates to the olink_qc_plot and olink_pca_plot functions (@simfor, #78)

BugFixes

Moved NEWS.md to correct level (@kathy-nevola, #74)
Added cran-comments.md file to document Notes for CRAN submission (@kathy-nevola, #74)
Update Vignette to reflect new functionality (@kathy-nevola, #78)

OlinkAnalyze 1.3.0

Major Changes

DESCRIPTION file updated to include all authors and maintainers (@kathy-nevola, #66)
Unit testing was added (@marisand, @simfor, #65, #55, #47)
Continuous Integration (CI) was added (@AskPascal, #57, #53, #40, #31)
read_NPX now converts Panel Names to Sentence case except Roman Numerals (@kathy-nevola, #44)
Output order of olink_bridgeselector() is now randomized (@marisand, #60)
PlateSize argument was added to displayPlateLayout() and olink_plate_randomizer for T48 and T96. Hardcoded sizes have been removed. (@marisand, #47)
Changed olink_pal() to have gray instead of light blue (@marisand, #22)

Bug Fixes

set_plot_theme() will now load Swedish Gothic Thin if available on all OS (@marisand, @AskPascal, #70, #39)
Help documentation was updated to correct typos and clarify notation for ANOVA and LME models (@kathy-nevola, @marisand,@AskPascal #67, #33, #37)
Fix olink_dist_plot() from showing multiple bars when sample has QC warning in some assays (@marisand, @AskPascal, #64)
Fix olink_qc_plot() from showing multiple points/labels when sample has QC warning in some assays (@marisand, @AskPascal, #63)
Panel names in npx_data1 and npx_data2 were fixed to match new read_NPX() formatting (@kathy-nevola, #62)
olink_bridgeselector() QC warning filtering changed to match olink_qc_plot() and olink_dist_plot() (@marisand, @AskPascal, #61)
global variables are now specified (@kathy-nevola, #45)
Function documentation updated to remove notes on R CMD check (@kathy-nevola, #39)
Fix summary casting "tukey" to "sidak" adjustment warning in olink_anova_posthoc() and olink_lmer_posthoc() functions (@marisand, #38)
Update functions to import selectively (@kathy-nevola, @Orbmac, @AskPascal, @marisand, #21, #20, #19, #18, #15, #29)
Fix guides size argument in olink_pca_plot() (#17) (@AskPascal, #24)