Deduce type of IGH reads
getIGHreadType.RdgetIGHreadType deduces, for each molecule in each cell identified via scanBam,
whether it corresponds to a productive (labelled "-P") or a sterile ("-S") IGH
molecule. A third category ("-C") is assigned if insufficient information is present
to distinguish "-P" and "-S".
Details
The function loops through each cell barcode - molecule barcode combination and looks for evidence of reads mapping to the following three regions: VDJ, C as well as the 5' intron to C. Each molecule is assigned based on these criteria:
Productive (-P) at least one read mapping to VDJ region and at least one read mapping to the C exonic region. NOTE: here we are not making the distinction of whether the VDJ has already been spliced to the C exons at the RNA level. We are simply asking whether the molecule can encode a Ig protein with both V and C regions.
Sterile (-S) at least one read mapping to the 5' intronic region to a C gene, without reads mapping to the VDJ region. These represent the 'sterile'/'germline' IgH transcripts which primes class-switch recombination.
A third category (-C) is assigned if insufficient information is available to classify the molecule in to the '-P' or the '-S' groups.