rescale: Function to rescale values based on quantiles

In bhklab/genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

Function to rescale values based on quantiles

Description

This function rescales values x based on quantiles specified by the user such that x' = (x - q1) / (q2 - q1) where q is the specified quantile, q1 = q / 2, q2 = 1 - q/2) and x' are the new rescaled values.

Usage

rescale(x, na.rm = FALSE, q = 0)

Arguments

x	The matrix or vector to rescale.
na.rm	TRUE if missing values should be removed, FALSE otherwise.
q	Quantile (must lie in [0,1]]).

Details

In order to rescale gene expressions, q = 0.05 yielded comparable scales in numerous breast cancer microarray datasets (data not shown).The rational behind this is that, in general, 'extreme cases' (e.g. low and high proliferation, high and low expression of ESR1, ...) are often present in microarray datasets, making the estimation of 'extreme' quantiles quite stable. This is specially true for genes exhibiting some multi-modality like ESR1 or ERBB2.

Value

A vector of rescaled values with two attributes q1 and q1 containing the values of the lower and the upper quantiles respectively.

See Also

base::scale()

Examples

# load VDX dataset
data(vdxs)
# load NKI dataset
data(nkis)
# example of rescaling for ESR1 expression
par(mfrow=c(2,2))
hist(data.vdxs[ ,"205225_at"], xlab="205225_at", breaks=20,
  main="ESR1 in VDX")
hist(data.nkis[ ,"NM_000125"], xlab="NM_000125", breaks=20,
  main="ESR1 in NKI")
hist((rescale(x=data.vdxs[ ,"205225_at"], q=0.05) - 0.5) * 2,
  xlab="205225_at", breaks=20, main="ESR1 in VDX\nrescaled")
hist((rescale(x=data.nkis[ ,"NM_000125"], q=0.05) - 0.5) * 2,
  xlab="NM_000125", breaks=20, main="ESR1 in NKI\nrescaled")

bhklab/genefu documentation built on Nov. 30, 2024, 9:03 p.m.