ComputeSteadyStateHalfLives {grandR}

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