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

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Documentation for package ‘SingleCellAlleleExperiment’ version 1.0.0

• 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