ComputeSteadyStateHalfLives: 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
)

Value

a new grandR object with an additional slot or analysis

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").