CalibrateEffectiveLabelingTimeMatchHalflives {grandR} | R Documentation |
Calibrate the effective labeling time by matching half-lives to a .reference
Description
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