identifyTSNs: Identify TSNs

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

Description

NOTE: This function is currently inactive and invisible to users of the pacakge. We may re-instate this function later, but for now, use identifyTSNsR to identify TSNs.

Usage

identifyTSNs(dat, nDistinctPause = 3, nCap = 1, widthTresh = 55,
  pLongCappedTresh = 0.25, factorDownsizeDataForPlot = 4,
  plotMe = TRUE)

Arguments

dat	a data.table containing results of a CoPRO experiment
nDistinctPause	number of distinct pause sites required
nCap	number of capped reads required
widthTresh	the transcript length after which pLongCappedTresh of reads must be capped
pLongCappedTresh	the fraction of reads greater than widthTresh in length that must be capped
factorDownsizeDataForPlot	the factor by which the size of the data is (randomly) reduced in generating the plot
plotMe	logical value indicating whether plots should be generated

Details

This function takes the results of a CoPRO experiment, stored in a data.table, and returns the set of TSNs present in the data. We use the following criteria to determine which nucleotides are TSNs: 1. 3+ pause positions and 1+ total capped reads 2. Reads > 55 nt are > 25 3. >= 15

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.