Compute pseudo NTRs from two count matrices

NTRs can be computed from given new and total counts.

Usage

ComputePseudoNtr(
  data,
  new.slot,
  total.slot = DefaultSlot(data),
  detection.rate = 1
)

Arguments

data

a grandR object

new.slot

the slot containing new RNA counts

total.slot

the slot containing total RNA counts

detection.rate

the detection rate of T-to-C mismatch reads (see details)

Value

a new grandR object

Details

To correct for some bias, a detection rate (as suggested by Cao et al., Nature Biotech 2020) should be provided. This detection rate defines, how much new RNA is detected on average using the T-to-C mismatch reads.