# S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes

## Documentation for package ‘SingleCellAlleleExperiment’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.scae | The SingleCellAlleleExperiment class
alleles2genes | Building first new subassay for SingleCellAllelexperiment object
check_valid_optional_package | Check package installation for optional functionalities
ext_rd | Extend rowData with new annotation columns
find_allele_ids | Identify rows containing allele information
genes2functional | Building second new subassay for the SingleCellAlleleExperiment object
get_agenes | Get immune gene rows
get_allelecounts | Get Subassay with allele gene names and raw allele quantification
get_knee_info | Knee plot info
get_ncbi_org | Get NCBI genes using the org.HS.db package
get_nigenes | Get non-immune rows
read_allele_counts | Reading in allele quantification data into SingleCellAlleleExperiment object
read_from_sparse_allele | Reading in allele-aware quantification data
rowData<--method | rowData setter for the SingleCellAlleleExperiment class
rowData<--method | rowData-NULL-setter for the SingleCellAlleleExperiment class
scae_subset | Subset SCAE object
scae_subset_alleles | Get allele rows
scae_subset_functional | Get functional class rows
show-method | Miscellaneous SingleCellAlleleExperiment methods
SingleCellAlleleExperiment | The SingleCellAlleleExperiment class
SingleCellAlleleExperiment-class | The SingleCellAlleleExperiment class
SingleCellAlleleExperiment-misc | Miscellaneous SingleCellAlleleExperiment methods