Description Usage Arguments Value Examples

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.

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

`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 “bins” (see below). |

`bins` |
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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
## 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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