Added new datasetssibship andhalfsib.In the app, these are available asExample1 andExample2, respectively.
The default genetic map, previously built-in to KLINK, has beenmoved to thenorSTR package under the namemap50, and is now imported from there.
KLINK now employs thespecial lumping methods recentlyimplemented inpedprobr andpedmut.This permits the use of complex mutation models(e.g. Stepwise) in most common pedigrees, includingpaternity and full/half siblings. In larger pedigrees, nonlumpablemodels are replaced with the simpler ‘Equal’ model.
TheLR table shown in the app has a new look,now using the same layout and marker order as the other tables. The “LRtable” sheet of the Excel download also uses this marker order.Note: TheReport sheets has not changed.
New app controlsEmpty markers (hide/show) andLikelihoods (hide/show/loglik) for the LR table in the appand the Excel download.
New app controlDecimals for setting the number ofdecimals in displayed tables.
Inconsistent marker names are handled more gracefully. Forinstance,Penta D,Penta.D,PentaD,PENTA D are now recognised as the samemarker (similarly for other markers, notablyPenta E andvWA).
TheMarker data table now excludes unused mutationmodel columns (app only).
The Excel download includes a new sheet,Plots,containing the two pedigree plots.
Added tooltips explaining app controls and tablecolumns.
Busy-indicator: A pulsating effect is now shown when the app isbusy.
Renamed columns in the linkage map:Chrom ->Chr andPosCM ->cM. Whenloading custom maps, variations of these names are accepted.
Only on shinyapp.io: Show banner warning about uploadingsensitive data.
Empty the.xml field when a new.famfile is loaded.
RStudio now stops the app when the user closes thebrowser.
Graceful handling of input without data.
TheMarker map control has been moved up to theInput app region.
Fixed a bug appearing when the input file contains an unmappedsingle marker.
Fixed a bug giving slightly incorrect LR values in some caseswhen a stepwise mutation model was used. This bug was related tolumping, which is now handled differently (see entry underNew features).
Modified the selection of markers for theUnlinked report. Within each pair, the marker with highestPIC value is chosen. For consistency, the PIC values used in thiscalculation are now always based on the same database(NorskDB_2024).
Minor tweaks of app appearance.
This version is a major update of both the KLINK package and theshiny app.
Expanded built-in genetic map covering 50 common STR markers, upfrom 18. Unlike the previous version, where linkage pairs were hardcoded, the markers are now dynamically paired up after data is loaded,ensuring more optimal use of the data.
The user may set a maximum linkage distance (cM), with the effectthat markers farther than this are considered unlinked.
Improved karyogram plot for clearer visualisation of markers andlinkage.
Improved readability of tables, using colours to indicate linkedmarkers.
New button “Reset” resetting all fields of the shinyapp.
New XML input field allowing the user to integrate data fromother sources (particularly: Amelogenin genotypes and IDinitials).
Updatepedprobr version to 0.9.3, giving muchfaster likelihood calculations in many cases.
Show wait cursor during LR calculations.
Use scientific format also for small LR totals in-app.
Unlinked report: Prioritise D5S2500 over D5S2800 if both arepresent, and similarly D10S2325 over D10S1435, and D19S253 over D19S433(reverses previous behaviour).
Fix typos in built-in linkage map.
Fix outdated mutation model in datasetpaternity.
Internal reorganisation, moving the Shiny code toinst/shiny/app.R.
launchApp() is now the main launching function, withrunKLINK() as an alias.
Fixes a minor regression error in the previous version.
New button “Mask” for downloading a masked version of thedataset.
Reading/writing.fam files is now handled by the newpackagepedFamilias(), which has been split out fromforrel.
Added R optionKLINK.debug which can be set to TRUEfor debugging (only when running KLINK from R).
Use (experimental)autoScale option in pedigreeplots.
Minor internal tweaks and bug fixes.
Although KLINK is primarily a Shiny app, the package nowdocuments and exports the main functions, enabling analysis in R aswell.
Added new datasetpaternity, with simulated data fora paternity case (including a mutation).
Improved formatting in output Excel document.
Simplified code in sync with recent pedsuite updates. The plotsmay appear slightly modified.
Add karyogram showing marker positions.
Add sheets “Unlinked” and “Linked only” in excel output.
Tweaked button placements.
New button letting the user choose fallback mutation model(applied when a model specified in the input file fails for whateverreason).
Fixed a couple of minor bugs
Added aNEWS.md file to track changes to thepackage.
pedtools version 2.2.0 is now required.
If the pedigrees prohibit arbitrary lumping, all complex mutationmodels are replaced with a simpler model. A notification to this effectis added when loading the file. This behaviour is currently triggered ifeither pedigree has an untyped nonfounder.