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metabolomicsR (version 1.0.0)

batch_norm: batch normalization

Description

Normalization data by the median value of each batch

Usage

batch_norm(
  object,
  feature_platform = "PLATFORM",
  QC_ID_pattern = "MTRX",
  test = FALSE,
  verbose = TRUE
)

Arguments

object

A Metabolite object. In the feature annotation slot `feature`, a platform column should be provided for metabolite measurement platform (eg. `PLATFORM`). The values in the `PLATFORM` column (eg. `Neg`, `Polar`, `Pos Early`, and `Pos Late`) are column names in the sample annotation `sample` to determine the batches of samples.

feature_platform

The column name of feature platform for metabolite measurements (eg. `PLATFORM`).

QC_ID_pattern

A character pattern to determine QC samples. Default value: "MTRX".

test

test the function for the first 20 columns.

verbose

print log information.

Value

A Metabolite object after normalization.

See Also

QCmatrix_norm