normalize_median: Median normalization

Description Usage Arguments Value See Also Examples

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

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## 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

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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.