ComputeSteadyStateHalfLives: Steady state half-lives for each sample

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Steady state half-lives for each sample

Description

Transforms each NTR to a half-life value (assuming steady state gene expression) and puts them into a new slot or adds an analysis

Usage

ComputeSteadyStateHalfLives(
  data,
  time = Design$dur.4sU,
  name = "HL",
  columns = NULL,
  max.HL = 48,
  CI.size = 0.95,
  compute.CI = FALSE,
  as.analysis = FALSE
)

Arguments

data	the grandR object
time	either a number indicating the labeling time, or a name of the Coldata table
name	the name of the new slot/analysis to put half-life values in
columns	which columns (i.e. samples or cells) to return; sets as.analysis to TRUE (see details)
max.HL	all values above this will be set to this
CI.size	A number between 0 and 1 representing the size of the credible interval
compute.CI	it TRUE, credible intervals are computed, this also sets as.analysis to TRUE
as.analysis	if TRUE add the results as analysis and not as data slot

Details

An NTR value p can be transformed into an RNA half-live using the equation log(2)/(-1/t*log(1-p)) This is described in our GRAND-SLAM paper (Juerges et al., Bioinformatics 2018).

Columns can be given as a logical, integer or character vector representing a selection of the columns (samples or cells). The expression is evaluated in an environment havin the Coldata, i.e. you can use names of Coldata as variables to conveniently build a logical vector (e.g., columns=Condition=="x").

Value

a new grandR object with an additional slot or analysis

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