Assessment of a cell-to-cell distance matrix with a metric of choice
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.
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).
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 “bins” (see below).
Intervals used to discretize the data in the case that Mutual Information distance (method="MI") is selected.
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
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## 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"]]
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