cast data frame IGH counts into a matrix

summariseIGHreads converts the data.frame of sterile/productive IGH molecules into a count matrix.

Usage

summariseIGHreads(tb, definitions)

Arguments

tb

A data.frame, output from getIGHreadType.

definitions

A list of GenomicRanges::GRanges object, each specifying the genomic coordinates of VDJ genes, C genes coding segments and sterile C transcripts. See the data objects 'human_definitions' and 'mouse_definitions' in the sciCSR package for formats.

Value

An array of cell barcode by IGH gene type (i.e. S/P/C per C gene)

Details

The function does a count of molecules classified to be Sterile (S), Productive (P) or C-only (C) for each isotype, over molecules per cell barcode and cast this count into a matrix of cell barcodes by IGH molecule type.