normalize_median: Median normalization

In jaehyunjoo/poplin: LC/MS Metabolomics Data Processing Utilities

Description

Apply median normalization to a matrix or poplin object. For each sample, feature intensities are divided by its median. The median of intensity values for individual samples will be one as a result.

Usage

## S4 method for signature 'matrix'
normalize_median(x, restrict = FALSE, rescale = FALSE)

## S4 method for signature 'poplin'
normalize_median(x, xin, xout, restrict = FALSE, rescale = FALSE)

Arguments

x	A matrix or poplin object.
restrict	Logical controlling whether any feature with missing values is excluded from the calculation of normalization factors.
rescale	Logical controlling whether the normalized intensities are multiplied by the median of normalization factors to make look similar to their original scales.
xin	Character specifying the name of data to retrieve from x when x is a poplin object.
xout	Character specifying the name of data to store in x when x is a poplin object.

Value

A matrix or poplin object of the same dimension as x containing the normalized intensities.

See Also

Other normalization methods: normalize_cyclicloess(), normalize_mad(), normalize_mean(), normalize_pqn(), normalize_scale(), normalize_sum(), normalize_vsn(), poplin_normalize()

Examples

data(faahko_poplin)

## poplin object
normalize_median(faahko_poplin, xin = "knn", xout = "knn_med")

## matrix
m <- poplin_data(faahko_poplin, "knn")
normalize_median(m, rescale = TRUE)

jaehyunjoo/poplin documentation built on Jan. 8, 2022, 1:13 a.m.