ComputePseudoNtr: Compute pseudo NTRs from two count matrices

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Compute pseudo NTRs from two count matrices

Description

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)

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.

Value

a new grandR object

grandR documentation built on April 4, 2025, 2:27 a.m.