dist: Customized Distance Function

In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

Description

Based on dist. Additionally it can handle correlation-based distances and has argument for imputation of NA distances. To avoid confusion with stats::dist all the default settings are such that it performs equivalently to the aforementioned one.

Usage

dist(x, method = "euclidean", na.avg = FALSE, ...)

Arguments

x	a numeric matrix
method	the distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "kendall", "spearman". Any unambiguous substring can be given.
na.avg	logical if yes, then NA distance will be imputed with average distance value. Default is FALSE.
...	arguments of dist

Note

In the current set-up corrlation values -1, 0 and 1 correspond to distances 1, 0.5 and 1, respectively.
R=1 -> dist=0
R=0 -> dist=0.5
R=-1 -> dist=1

Examples

x <- matrix(c(1:5, 5:9, 9:13), ncol=3)
stats::dist(x)
dist(x)
dist(x, method="pearson")

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.