Movatterモバイル変換

Version 1.3.0: October 5,2023

General:

Updated dependencies alakazam >= 1.3.0, shazam >= 1.2.0,ggplot2 >= 3.4.0.
Added alocus column to the package’s example data, tosatisfy alakazam >= 1.3.0 requirements.

Bug fixes:

Fixed a bugdefineClonesScoper where the bulk clonalclustering was using light chain sequences. Now, light chain sequencesare removed based on thelocus information. If the columnlocus does not exist, it is created withalakazam::getLocus(v_call).
Fixed a bug indefineClonesScoper where thesplit_light part of the algorithm was reanalyzing heavychain v_calls and using this information to sometimes split clone_idgroups into subgroups. Only light chain v_calls should be used for this.The bug could be observed in situations wherefirst=FALSEand the ‘linker’ ambiguous heavy chain v_calls were left out of the sameclone_id group because of the junction distance threshold.
Fixed parallelization setup fordefineClonesScoper.

General:

General:

Updated dependencies to R >= 4.0, ggplot2 >= 3.3.4, dplyr>= 1.0, alakazam >= 1.2.0, and shazam >= 1.1.0.
Changed the internal definition of degenerate characters fromN to any characters except[ATCG].

Cloning:

Addedfields argument toidenticalClones,hierarchicalClones andspectralClones to allowfor data partitioning prior to clonal assignment.
Fixed a bug in the cloning functions causing an error in single-cellmode when the input data contains only heavy chains.

Fixed a bug in the clonal clustering methods causing TCR data tofail.
Added support for single-cell data in the clonal clustering methods,which are enabled by defining the optionalcell_idcolumn.

Fixed a fatal error inidenticalClones,hierarchicalClones andspectralClones whenspecifyingnproc > 1.

Backwards Incompatible Changes:

Changed default expected data format from the Change-O data formatto the AIRR Rearrangement standard. For example: where functions usedthe column nameV_CALL (Change-O) as the default toidentify the field that stored the V gene calls, they now usev_call (AIRR). That means, scripts that relied on defaultvalues (previously,v_call="V_CALL"), will now fail ifcalls to the functions are not updated to reflect the correct value forthe data. If data are in the Change-O format, the current default valuev_call="v_call" will fail to identify the column with the Vgene calls as the columnv_call doesn’t exist. In thiscase,v_call="V_CALL" needs to be specified in the functioncall.
ExampleDb converted to the AIRR Rearrangement standardand examples updated accordingly.
SplitdefineClonesScoper function to three functions:identicalClones,hierarchicalClones, andspectralClones.

General:

Cloning:

Fixed a platform precision incompatibility bug which caused spectralcloning results to be non-reproducible across platforms.
Added largest distance-to-nearest filter to clustering process.

Deprecated:

functionanalyzeClones is deprecated. The clonalanalysis has been added to the main functiondefineClonesScoper as an argumentanalyze_clones.
the out put class is deprecated. Results would be reported as a listif argumentanalyze_clones set to be true, otherwise asingle dataframe is returned.
plot_neighborhoods from clonal analysis has beendeprecated.
neighborhoods from clonal analysis has beendeprecated.

General:

New models,hierarchical for hierarchical-clusteringbased, andidentical for clustering among identicaljunction sequences are added.
New method for spectral-clustering based model has been addedthrough thevj in argumentmethod.

Clonal analysis:

Switched the meaning of the “inter” and “intra” labels incalculateInterVsIntra function. Now, “inter” is the labelused to form distances that mean between clones, and “intra” is thelabel used to form distances that mean on the inside, within eachclone.
Changed theplotInterVsIntra output from a density plotto a histogram.
Changed the way to calculate the effective threshold. Now, desntiyapproach is used.

Initial public release.