neighborhood_sortingcost: A cost computation function for Neighborhood algorithm

In JinmiaoChenLab/uSORT: uSORT: A self-refining ordering pipeline for gene selection

Description

A cost computation function for Neighborhood algorithm

Usage

neighborhood_sortingcost(expr = NULL, sigma_width = 1,
  method = c("Euclidean", "Correlation", "eJaccard", "none"))

Arguments

expr	An expresssion matrix containing n-rows of cells and m-cols of genes.
sigma_width	An integer number determining the degree of spread of the gaussian distribution which is used for computing weight matrix for Neighborhood sorting method.
method	A character string indicating the distance function.

Value

A numeric value of sorting cost.

Examples

set.seed(15)
da <- iris[sample(150, 150, replace = FALSE), ]
d <- da[,1:4]
randomOrdering_cost <- neighborhood_sortingcost(d, method= 'Euclidean')
randomOrdering_cost

da <- iris
d <- da[,1:4]
properOrdering_cost <- neighborhood_sortingcost(d, method= 'Euclidean')
properOrdering_cost

JinmiaoChenLab/uSORT documentation built on May 7, 2019, 10:53 a.m.