Calibrate the effective labeling time by matching half-lives to a .reference

The NTRs of each sample might be systematically too small (or large). This function identifies such systematic deviations and computes labeling durations without systematic deviations.

Usage

CalibrateEffectiveLabelingTimeMatchHalflives(
  data,
  reference.halflives = NULL,
  reference.columns = NULL,
  slot = DefaultSlot(data),
  time.labeling = Design$dur.4sU,
  time.experiment = NULL,
  time.name = "calibrated_time",
  n.estimate = 1000,
  verbose = FALSE
)

Arguments

data

A grandR object

reference.halflives

a vector of reference Half-lives named by genes

reference.columns

the reference column description

slot

The data slot to take expression values from

time.labeling

the column in the column annotation table denoting the labeling duration or the labeling duration itself

time.experiment

the column in the column annotation table denoting the experimental time point (can be NULL, see details)

time.name

The name in the column annotation table to put the calibrated labeling durations

n.estimate

the times are calibrated with the top n expressed genes

verbose

verbose output

Value

A new grandR object containing the calibrated durations in the column data annotation

See also

FitKineticsGeneSnapshot