KNC: k-nearest class means (KNC)

In DavisLaboratory/msImpute: Imputation of label-free mass spectrometry peptides

k-nearest class means (KNC)

Description

The fraction of k-nearest class means in the original data that are preserved as k-nearest class means in imputed data. KNC quantifies preservation of the mesoscopic structure after imputation. Requires complete datasets - for developers/use in benchmark studies only.

Usage

KNC(xorigin, ximputed, class, k = 3)

Arguments

xorigin	numeric matrix. The original log-intensity data. Can contain missing values.
ximputed	numeric matrix. The imputed log-intensity data.
class	factor. A vector of length number of columns (samples) in the data specifying the class/label (i.e. experimental group) of each sample.
k	number of nearest class means. default to k=3.

Value

numeric The proportion of preserved k-nearest class means in imputed data.

Examples

data(pxd007959)
y <- pxd007959$y
y <- y[complete.cases(y),]
# for demonstration we use same y for xorigin and ximputed
KNC(y, y, class = as.factor(pxd007959$samples$group))

DavisLaboratory/msImpute documentation built on Jan. 5, 2024, 3:50 a.m.