Genotype cells at the VDJ recombination sites
genotype_vdj(cnr, gene.type.column = "gene_biotype")
a cnr bundle. gene.index MUST include a column named 'gene.type' with pattern "TR.*gene" for T-cell receptor genes, and "IG.*gene" for B-cell receptor genes. These are the defaults for gene.type in bioconductor::biomaRt
name of gene type column
Returns a CNR object with 'cell.type' column containing assigments for 'T-cell', 'B-cell', and 'vdj.unspecified'. The function will only annotate cells with deletions on a 'TR' or 'IG' gene present in the gene.index table. All other annotation will be left intact. If 'cell.type' column is not present one will be created with 'NA'.
An additional cnr[["vdj.cells"]] vector is also returned containing the cell type of only VDJ cells.
data(cnr) cnr <- genotype_vdj(cnr)
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