identifyTSNsR: Identify TSNs using the R column

In Timothy-Barry/coproanalysis: Analyze CoPRO and Related Data

Description

This function is similar to the identifyTSNs function. The difference is that the capped + uncapped library (the R column) is used to define TSNs. We have the following requirements. 1. 3 + pause positions. 2. 5 + total reads.

Usage

identifyTSNsR(dat, nDistinctPauseThresh = 3, nReadsThresh = 5,
  plotMe = FALSE)

Arguments

dat	a data.table containing results of a CoPRO experiment
nDistinctPauseThresh	number of distinct pause sites required
nReadsThresh	number of total cappped + uncapped (R) reads required

Value

a vector containing the nucleotides (indexed by ID5) that qualify as TSNs according to the above criteria.

Timothy-Barry/coproanalysis documentation built on Feb. 12, 2020, 7:33 a.m.