getters {conclus} | R Documentation

## getters

### Description

Retrieve the data of the slots of a scRNA-seq, Tsne or Dbscan object.

### Usage

    getExperimentName(theObject)

    getCountMatrix(theObject)

    getSceNorm(theObject)

    getSpecies(theObject)

    getOutputDirectory(theObject)

    getTSNEList(theObject)

    getDbscanList(theObject)

    getSuggestedClustersNumber(theObject)

    getCellsSimilarityMatrix(theObject)

    getClustersSimilarityMatrix(theObject)

    getClustersSimilarityOrdered(theObject)

    getMarkerGenesList(theObject, cluster)

    getTopMarkers(theObject)

    getGenesInfos(theObject)

    ## S4 method for signature 'Tsne'
    getName(theObject)

    getPerplexity(theObject)

    getPC(theObject)

    getCoordinates(theObject)

    getName(theObject)

    getEpsilon(theObject)

    getMinPoints(theObject)

    getClustering(theObject)

### Arguments

`theObject` | A scRNA-seq, Tsne or Dbscan object. See description or ?scRNAseq, ?Tsne, ?Dbscan.
`cluster` | Integer, index of the cluster to retrive the gene list. If cluster="all", get the marker list for each cluster into a list.

### Value

getExperimentName: Get the name of the experiment (scRNA-seq).

getCountMatrix: Get the count matrix (scRNA-seq).

getSceNorm: Get the SingleCellExperiment object used (scRNA-seq).

getSpecies: Get the species (scRNA-seq).

getOutputDirectory: Get the path of the output directory (scRNA-seq).

getTSNEList: Get the list of Tsne objects (scRNA-seq).

getDbscanList: Get the list of Dbscan objects (scRNA-seq).

getSuggestedClustersNumber: Get the suggested clusters number (scRNA-seq).

getCellsSimilarityMatrix: Get the cell similarity matrix (scRNA-seq).

getClustersSimilarityMatrix: Get the cluster similarity matrix (scRNA-seq).

getClustersSimilarityOrdered: Get the clusters ordered by similarity (scRNA-seq).

getMarkerGenesList: Get the list of marker genes by clusters (scRNA-seq).

getTopMarkers: Get the most significant markers by clusters (scRNA-seq).

getGenesInfos: Get informations about marker genes (scRNA-seq).

getPerplexity: Get the perplexity used (Tsne).

getPC: Get the PC used (Tsne).

getCoordinates: Get the matrix of tSNE coordinates (Tsne).

getName: Get the name of the tSNE or Dbscan object (Dbscan).

getEpsilon: Get the epsilon used (Dbscan).

getMinPoints: Get the MinPoint used (Dbscan).

getClustering: Get the matrix of DBSCAN clustering (Dbscan).

### Author(s)

Ilyess RACHEDI

### Examples

    ## Load the count matrix
    countMatrixPath <- system.file("extdata/countMatrix.tsv", package="conclus")
    countMatrix <- loadDataOrMatrix(file=countMatrixPath, type="countMatrix",
                                    ignoreCellNumber=TRUE)

    ## Load the coldata
    coldataPath <- system.file("extdata/colData.tsv", package="conclus")
    columnsMetaData <- loadDataOrMatrix(file=coldataPath, type="coldata",
                                        columnID="cell_ID")

    ## Create the initial object
    scr <- singlecellRNAseq(experimentName = "Bergiers",
                    countMatrix     = countMatrix,
                    species         = "mouse",
                    outputDirectory = "YourOutputDirectory")

    experimentName <- getExperimentName(scr)
    countMatrix <- getCountMatrix(scr)
    species <- getSpecies(scr)
    outputDirectory <- getOutputDirectory(scr)

[Package conclus version 1.2.4 Index]