partialDist: Partial distance matrix (focus on closest)

In wrMisc: Analyze Experimental High-Throughput (Omics) Data

Partial distance matrix (focus on closest)

Description

partialDist calculates distance matrix like dist for 1- or 2-dim data, but only partially, ie only cases of small distances. This function was made for treating very large data-sets where only very close distances to a given point need to be found, it allows to overcome memory-problems with larger data (and faster execution with > 50 rows of 'dat').

Usage

partialDist(
  dat,
  groups,
  overLap = TRUE,
  method = "euclidean",
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

dat	(matrix of numeric values) main input
groups	(factor) to split using cut or specific custom grouping (length of dat)
overLap	(logical) if TRUE make groups overlapping by 1 value (ie maintain some context-information)
method	'character' name of method passed to dist
silent	(logical) suppress messages
debug	(logical) display additional messages for debugging
callFrom	(character) allow easier tracking of message(s) produced

Value

This function returns a matrix with partial distances (not of class 'dist' object)

See Also

dist

Examples

set.seed(2016); mat3 <- matrix(runif(300),nr=30)
round(dist(mat3), 1)
round(partialDist(mat3, gr=3), 1)

wrMisc documentation built on Nov. 17, 2023, 5:09 p.m.