CalibrateEffectiveLabelingTimeMatchHalflives {grandR} | R Documentation |
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.
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
)
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 |
A new grandR object containing the calibrated durations in the column data annotation