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Normalise to starting time point

Source: R/normalise_to_start.R
normalise_to_start.Rd

Normalise to starting time point, to make the mean of starting time point samples 0.

Two modes are available:

  • by_subject = FALSE (default): computes the group-level mean at the first non-NA time point per feature and subtracts it. All samples within a group share the same baseline.

  • by_subject = TRUE: computes each subject's value at the first non-NA time point per feature and subtracts that subject-specific baseline. Removes between-subject baseline differences. Use when each subject has their own initial condition. Requires a Subject column in colData.

Usage

normalise_to_start(se_obj, by_subject = FALSE)

Arguments

se_obj

A SummarizedExperiment object created by create_input()

by_subject

If FALSE (default), use group-level baseline. If TRUE, use subject-level baseline (requires Subject column in colData).

Value

A SummarizedExperiment object with normalised data in the second assay slot.

Examples

data(example_obj)
example_obj <- normalise_to_start(example_obj)
#> Normalising to group baseline at each feature's first non-NA time point.