sc_distanceObj: Assessment of a cell-to-cell distance matrix with a metric of...

In sincell: R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

Description

Function to assess a cell-to-cell distance matrix from a gene expression matrix with a metric of choice among the following: Euclidean distance, Mutual Information, L1 distance (Manhattan distance), Pearson correlation or Spearman correlation.

Usage

sc_distanceObj(SincellObject, method="euclidean", bins=c(-Inf,0,1,2,Inf))

Arguments

SincellObject	A SincellObject named list as created by function sc_InitializingSincellObject with a named member "expressionmatrix" containing a numeric matrix that represents a gene expression matrix gathering the expression levels of each single-cell in the experiment (displayed by columns) for each detected gene (displayed by rows).
method	Distance method to be used. The available distances are the Euclidean distance (method="euclidean"), Manhattan distance (also called L1 distance, method="L1"), cosine distance (method="cosine") , distance based on Pearson (method="pearson") or Spearman (method="spearman") correlation coefficients, and distance based on Mutual Information (method="MI"). Intervals used to assess Mutual Information are indicated in the parameter <e2><80><9c>bins<e2><80><9d> (see below).
bins	Intervals used to discretize the data in the case that Mutual Information distance (method="MI") is selected.

Value

A SincellObject named list whose members are: expressionmatrix=SincellObject[["expressionmatrix"]], cell2celldist=cell2celldist,method=method,bins=bins, where "cell2celldist" contains the numeric matrix representing the cell-to-cell distance matrix assessed by sc_distanceObj with the indicated parameters

Examples

## Generate some random data
Data <- matrix(abs(rnorm(3000, sd=2)),ncol=10,nrow=300)

## Initializing SincellObject named list
mySincellObject <- sc_InitializingSincellObject(Data)

## To access the gene expression matrix
expressionmatrix<-mySincellObject[["expressionmatrix"]]

## Distance
mySincellObject<-sc_distanceObj(mySincellObject)
mySincellObject<-sc_distanceObj(mySincellObject, method="MI",bins=c(-Inf,0,2,4,6,8,Inf))
mySincellObject<-sc_distanceObj(mySincellObject, method="spearman")

## To access the cell-to-cell distance matrix
cell2celldist<-mySincellObject[["cell2celldist"]]

sincell documentation built on Nov. 8, 2020, 5:58 p.m.