Changes regarding the second round of comments during the Bioconductor submission review:
Minor changes to SCAE-show method
Extended and moved installation-checks for packages used in optional functionalities to the SCAE-constructor
Extended checks for the rowData setter
Extended unit tests to increase coverage
Changes regarding the first round of comments during the Bioconductor submission review:
Removed multiple dependencies, now listed as suggested
computation of the logcounts assay now optional
computation of a knee plot and according inflection/knee points now optional
computation of new gene-symbols now optional
minor changes in tests (needs to be extended to test for new optional code); also extension of the tests to check new code
major changes in package structure and organisation
reworked vignette to include optional features
scaeData which also affected this package.The package is defining a S4 class that is extending the SingleCellExperiment class. The multi-layer data structure integrates data for immune genes at allele and functional level.
Workflow: To be able to generate a SingleCellAlleleExperiment object the data has
to be generated by the connected workflow single-cell ImmunoGenomic Diversity (scIGD)
which performs allele typing and quantification of genes and typed alleles.
Use the read_allele_counts() function to read in the data and generate an
SCAE object. This function also offers parameters to perform filtering on the data,
as well as visualize the filtering step in a so called knee plot.